One of PETA's philosophical guidelines is that no animals should be pets, that keeping animals as pets is slavery and they all belong back out in the wild. I'm sure they can totally justify the killing to themselves because of that, especially since they've been criticized for the cruelty of throwing animals out into the wild who weren't prepared for it and subsequently died of starvation, injury, etc. If keeping animals in captivity is morally wrong but putting those individuals into the wild would result in their slow and/or painful deaths, then killing them quickly would seem like the better choice.

Anyone who has pets and gives money to PETA should really think about these things.