I'll restate your question with my words to see if I've understood it properly first.
Let's keep the math easy. ECL 2, starting level 2 (1000 XP)
You get a +2 LA somewhere during level 2, let's say right after leveling up.
So you're now 1000 XP, ECL 4 and you need to reach ECL 5 for adding your new class level.
Your DM says ECL 5 is reached at 10k XP so you now need 9k XP to level up.
You say LA +2 is like going from 4 to 5 so you need 4k XP to level up.
Your way, you gained two levels (your LA) for free.
DM's math: 0 + 1000 + 2000 + 3000 + 4000 = 10k
Your math: 0 + 1000 + ............. 4000 = 5k
Your DM is right and no, it's not like you need more XP the higher you get, because your class levels you already took costed you less than if you took them after the template, so the thing balances out. The only real imbalance comes from the fact that you get the template before paying the XP for that LA.
As for the example you quoted, I'm pretty sure that was a typo and that's 9000 XP, not 3000
Up front, let me just suggest that this character is offensively devastating, but is frighteningly vulnerable (LA does that), and useless outside of combat. Moreover, these low levels are very much the best time to be playing this character. Depending on the pace of the game, it may be best to let him just enjoy it while it lasts. Unfortunately, it likely won’t last long. See an earlier answer about an overly strong barbarian.
But I think we can do better than you have here. You see, being devastating offensively, but shockingly vulnerable and useless out of combat, does cause a lot of problems. LA causes a lot of problems, but the biggest one is exactly this: skew.
A simple improvement, in both directions, by suggesting the LA +1 goliath from Races of Stone—less LA, less power, and the character is less skewed and causes fewer problems. The goliath isn’t Large, but has powerful build that lets them count as Large in many ways—and then the goliath barbarian substitution level, also in Races of Stone, offers mountain rage, and truly-Large size for a limited amount of time per day. Having the player use the goliath’s stats, despite being a “half-ogre,” would be a straightforward solution with WotC support.
But really, I think we can do even better than that. The goliath isn’t a half-ogre, and powerful build isn’t Large size, and while mountain rage can cover most uses, it still isn’t quite the same. And in my experience, having played, played alongside, or run games for goliath barbarians in the past... the goliath doesn’t really earn its LA either, even with mountain rage. So what I propose is an LA +0 half-ogre. True Large size, while very very good, might be possible on an LA +0 race.
Therefore, I present an LA +0, Large size, half-ogre race. Races are relatively simple parts of the game, and I have designed races professionally for 3.5e and Pathfinder; I am reasonably confident in my design here. It goes off the established rails some (LA +0 Large size is verboten under WotC design guidelines, and even powerful build always came with LA +1), but I’m going to build in a lot of downside. Moreover, I have played (with) plenty of characters that were Large—it isn’t that big a deal. Even in gestalt games where the LA could all be put on one side (greatly mitigating the effect of the LA and making half-ogre et al. far cheaper to use), the Large size was only “good,” not “broken.” (The large ability score adjustments were far more problematic.) I am confident that the drawbacks of this race are at least as costly as the effort expended by those characters in becoming Large.
Half-Ogre Racial Traits
Starting Ability Score Adjustment: +2 Str, −2 Dex, −2 Int, −2 Cha.
Large: As Large creatures, half-ogres have a −1 penalty to Armor Class and a −1 penalty on all attack rolls. They also have a reach of 10 feet.
Speed: Half-ogre land speed is 30 feet.
Darkvision: Half-ogres have darkvision with a range of 60 feet.
Giant Blood: For all special abilities and effects, a half-ogre is considered a giant. Half-ogres can use giant weapons and magic items with racially-specific giant powers as if they were giants.
Automatic Languages: Giant and Common. Bonus Languages: Draconic, Gnoll, Goblin, Orc, and Abyssal.
Favored Class: Barbarian.
Level Adjustment: +0.
By drastically reducing the ability score bonuses and removing the natural armor, we reduce a lot of the skew in the character. And because the ability score adjustments turn out sharply negative, and the race really doesn’t have much of anything else going on, we attach some very heavy drawbacks on the Large size. I considered losing the darkvision (after all, ogres have both that and low-light vision, and Savage Species saw fit to toss out the low-light vision), but in my experience darkvision is minor in most cases, and the race block just looked bare without it. But it might be a target if you want to remove more.
Ultimately, this race ends up being very, very good for a barbarian, and several other classes (the lack of Wisdom penalty opens up interesting opportunities for, say, psychic warrior), but it doesn’t end up being necessarily the best option every time. That is, it joins the top tier of race options for melee characters, but it doesn’t establish an entirely new tier over and above a few of the best existing options. Dragonborn, human (and human variants), warforged, water orc are each competitive, for examples. A dragonborn half-ogre could be a problem (since you keep the best thing about half-ogre and then get real racial features from dragonborn), but no more so than a dragonborn warforged—so you should probably just ban both of those combinations (or allow both, but recognize that they start to look like the only reasonable melee options).
Best Answer
Note: This answer is primarily from a 3.5e perspective. Changing this to a 3e perspective doesn't change much so far as I'm aware.
It's not as good a deal as it seems
Bobbi the Builder, a level 13 wizard who possesses the feats Craft Wondrous Item (Player's Handbook 92–3) and Craft Magic Arms and Armor (PH 92), labors for a month in a 500-gp laboratory. During that time, she also succeeds on her Craft (armorsmithing) skill check (DC 20) to sculpt from 500 lbs. of pure iron a magical iron golem limb (Monster Manual II 209). To finish the rituals needed for the limb's creation, she spends 20,000 gp on raw materials and 400 XP, and casts the 5th-level Sor/Wiz spells cloudkill [conj] (PH 210) and 6th-level Sor/Wiz spell geas/quest [ench] (PH 234–5). She puts the limb in her Heward's handy haversack (Dungeon Master's Guide 259) (2,500 gp; 5 lbs.) in case of an emergency.
Attaching the limb
While on an adventure, there's an emergency: Abe the Unlucky reaches into a sphere of annihilation (DMG 279) (minor artifact; 0 lbs.) and, rather than "suck[ing Abe] into the void, [leaving him] gone, and utterly destroyed," the DM rules that only Abe's arm is utterly destroyed. Traumatized, Abe looks at his stump, whimpers, and collapses. (Limb loss in 3.5e is typically at the DM's discretion.)
"I've got this," says Bobbi, and she whips out the iron golem arm. (That she has an arm is enough; handedness, fortunately, isn't really an issue in 3.5e.) She takes a standard action to attach the golem limb where Abe's original limb once was. That's because
This is Abe's first iron golem limb and, after it's attached, his body'll never be able to accept a different kind of golem limb. When the golem limb's attached, Abe makes a Will saving throw (DC 15).
Making the saving throw
Contrary to popular belief, a creature cannot opt to fail saving throws against anything. Creatures can voluntarily fail saving throws against spells (and, by extension, spell-like and supernatural abilities, which are like spells but with exceptions) and a few other similar cases (like psionics) and edge cases (like drugs), but the Will saving throw mandated by the golem limb is neither spell, similar case, nor edge case, so Abe can't opt to fail. (A creature can have effects applied to it to reduce its chance of success on a saving throw, but a 20 will still succeed… except in 3e, where a natural 20 on a saving throw isn't an automatic success nor a natural 1 an automatic failure.)
If Abe succeeds on the Will saving throw, he's gained a pretty significant amount of power asymmetrically: he gains the half-golem template except he retains his own type and gains a +4 bonus to his Constitution score. (And, as the template includes a golem's magic immunity, he'll likely need this power unless the DM allows Abe to lower an immunity voluntarily, an act legal according to one parenthetical example abesent from the SRD on Voluntarily Giving Up a Saving Throw (PH 79) yet nowhere else in entire D&D 3.5e corpus.)
If Abe fails the Will saving throw, the text makes it sound like Abe should become an NPC. That's because failing the saving throw means Abe
Nonetheless, a DM could still let a player continue playing such a character in an atypical adventuring party. However, the Monster Manual II on Effective Character Level, in part, says
And, while some creatures in the Monster Manual II do have an ECL, the template half-golem has no general ECL entry, and the sample half-golems—all of them constructs that, apparently, failed the golem limb attachment Will saving throw—from the Monster Manual II (209–12) and its Web enhancement "More Half-golems!" (1–5) don't have an ECL either. They just don't appear to be appropriate for PCs, despite their Advancement entries. (The D&D v.3.5 Accessory Update lists the LA of the Monster Manual II's printed half-golem templates as LA —, and "creatures suitable for use as player characters or as cohort" have an entry that's not LA — according to the Monster Manual (7) for 3.5e. So in 3.5e such creatures really aren't appropriate for PCs.)
Incarnating afterward
Thus this DM assumes that slapping a golem limb on a dude is legit, and the creature, if a PC, remains playable. The downside of magic immunity (if it can't be lowered and, perhaps, even if it can) is such a significant impairment that getting a metric crapton of bonuses is necessary for the PC to continue adventuring at all, and, even then, probably not for long once the novelty wears off. Note that this PC is an ineligible target for the 9th-level Sor/Wiz spell incarnate construct [trans] (Savage Species 67–8).
However, this DM can't imagine a creature that wants "to slaughter as many flesh creatures as possible" agreeing to fail the saving throw against the spell incarnate construct. Okay, this DM can contrive a scenario where that might be a thing ("By taking on a fleshy form, I shall be able to fit in better among the fleshy and slay more of the fleshy! Muhaha!"), but the half-golem's magic immunity (if it can't be lowered) will negate the spell incarnate construct anyway. Yet the existence of the incarnate stone golem (SS 120–1) means someone found a way to cast the spell on that stone golem, so maybe this half-golem could find that caster…
But that's really complicated. In short, a PC could get a golem limb, fail the Will saving throw, and become an NPC. Then that NPC could find a creature who can cast the spell incarnate construct in such a way as to bypass the NPC's magic immunity and become eligible for PC status once more, but the DM must determine that PC's ECL. This DM suggests that this ECL be the PC's Hit Dice −2. The template incarnate construct removes most of the PC's special abilities, including all special attacks and special qualities, which is pretty much everything previously gained from class levels.