Keeping it down is easy
Dealing continual damage will keep the Big T down for the count as long as you want to keep it down. Drowning him or placing him in an environment that causes continual damage that he can't resist (or something more exotic - Positive Energy Plane?) can do the same job. Big T can't burrow, so you can drop him in a deep hole (dug with magic, probably) and then cave it in on him.
Making Him Dead, Though...
Essentially you'd need a way to strip him of the regeneration trait entirely. 3.5 had a psuedo-poison (Trollbane) that would suppress Big T's regeneration, but that content isn't available in Pathfinder and furthermore their version of the Big T ignores it by virtue of your quoted text. Without a way to strip the ability entirely the best you can really do is kill him, summon a small army of flying things that don't need to breathe, and ask them to drop him off in the vacuum of space.
And Requested By Comment
Further clarification on the Positive Energy Plane was requested, so:
The Tarrasque is not immune to being blown up by the Positive Energy Plane, though it is immune to dying thereby. Dropping him into the Plane is mostly to get rid of him from your dimension; lacking a native way out, he heals, overheals, and then 'dies', returning to 1 hit point to restart the cycle. The Negative Energy Plane isn't as useful because the Tarrasque regenerates the damage it's dealt every round, and even if it comes into contact with some aspect capable of killing it instantly Big T's Fort save is more than sufficient to protect it.
The spell animate dead usually applies to the targeted corpse the template skeleton or the template zombie
There's probably not going to be any direct developer support for or against your GM's ruling, likely because the developers considered the actual rules so obvious there was no reason to make such a ruling.
The spell animate dead targets one or more corpses, not specifically humanoid corpses and not mandating the resultant creatures be, for example, humanoid skeletons. Further,
- A zombie can be created only from a mostly intact corpse.
- A skeleton can be created only from a mostly intact corpse or skeleton.
The spell says nothing about transforming a corpse from the corpse of the original creature into the corpse of a humanoid. The template skeleton provides several examples of nonhuman skeletons, and the template zombie does the same. Seriously, all evidence points to, for example, a mostly intact 9 Hit Die green dragon corpse becoming either a 9 Hit Die green dragon skeleton or a 9 Hit Die green dragon zombie when such a corpse is the target of the spell animate dead (and requiring the expenditure of 225 gp of onyx as material components).
So, while it's hilarious to imagine, for example, a wizard casting the spell animate dead on the mostly intact skeleton of a vicious advanced megaraptor and ending up not with an advanced megaraptor skeleton but a 1 Hit Die humanoid skeleton, or a wizard casting the spell animate dead on the mostly intact corpse of a crocodile and ending up not with a zombie crocodile but a generic humanoid zombie, that's also deeply weird.
By the way, prior to this question, I'd never considered any other way of interpreting the spell animate dead except to animate monster corpses as monster corpses, but, as evidenced by this 2010 EN World thread, at least one other GM uses a similar house rule to your GM's house rule. (Or maybe that question's also about your GM's animate dead house rule? [Cue dramatic music.])
Working around these limits anyway
However, even if the GM insists that the spell animate dead when used to make skeletons or zombies only creates 1 Hit Die humanoid skeletons or zombies, options remain. The spell animate dead can turn a big ol' pile of those 1 Hit Die humanoid skeletons or zombies into a necrocraft, or the spell can make an isitoq or a beheaded. It will be difficult for the GM to argue against these alternatives given such creatures' descriptions' increased specificity.
These alternatives are just samples. The more bestiaries available, the more options multiply.
Best Answer
As GM, you always have more options than you think, and you should always try to choose the one that's the most fun. My vote would be for the following:
4. This infuses the tarrasque with negative energy, creating an eldritch horror that threatens all of existence.
The rules don't say exactly where the tarrasque came from or how it works, but it's safe to assume that the creature is powered by some unlimited source of magic energy deep within its hulking form. The animate dead spell will corrupt this power source with negative energy, creating a threat to existence itself.
The most immediate effect will be the creation of an undead creature much more powerful than the original tarrasque, and certainly not under the control of the PC necromancer. The power of this creature will only grow over time as its power source becomes more corrupt. The creature will emit a negative energy aura that extends for miles, granting many permanent negative levels to creatures who fail their save and transforming most living creatures in the area to undead. As the creature's power grows, nightshades will begin to come forth from the negative energy plane to join with it, and it will begin to emit waves of negative energy of increasing radius. All natural healing of living creatures will cease, the dead will begin to rise from their graves, and material plane will begin to merge with the plane of negative energy.
It's up to the PCs to find out where the original tarrasque came from and how they can undo the damage that they have done. They might also have to deal with powerful planar beings who would use the abomination for their own ends, or who hope to defend the multiverse from the threat now posed by the material plane.