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

So by the rules, lycanthropy is neither a curse nor a disease; it’s a template. The “curse of lycanthropy” is really a curse that causes you to gain the template—the point being, once the template is applied, the curse isn’t really a part of the equation. Similarly, for all lycanthropy spreads “like” a disease, it isn’t one. This is why the curing lycanthropy section needs all these special rules for handling it—it isn’t your standard curse or disease. The spells break enchantment, heal, remove curse, and remove disease don’t normally do anything to a template, hence that section.

The section does not, however, address immunity. The template itself kind-of addresses the concern when creating a lycanthrope in the first place:

“Lycanthrope” is a template that can be added to any humanoid or giant (referred to hereafter as the base creature).

But templates are not removed if the creature would later become ineligible to receive them (indeed, many templates make changes to the creature that would invalidate themselves, so it would be a problem if they did). So while an undead creature is not allowed to become a lycanthrope (they have the undead type, not the humanoid or giant type), a lycanthrope could become undead—and nowhere is this mentioned as ending the lycanthropy.

Now, in your world, you could reasonably rule that lycanthropy is enough “like a disease” to not apply to the undead, or that it is otherwise incompatible with lycanthropy. But you could also very justifiably rule the opposite way, and that ruling is more consistent with the rules, both in their technicalities and also (I would argue) in their spirit.