I don’t know that all vegetarianism is apikorsus, but I understand why someone might think so; it’s more than mere stupidity. Rishonim say (IIRC, there’s a Rashb”a) that someone who doesn’t believe in the words of Chazal is an apikores. Now, if Chazal’s value system was such that human need takes priority over tzaar baalei chaim, and someone comes along and says no, we gave no moral right to benefit from something which causes tzaar to an animal, I think he is a kofer b’divrei Chazal.
Yes, Chazal believed in being compassionate to animals; in fact, tzaar baalei chaim is d’Oraisa according to many. It has its parameters and limitations, though, and one who thinks he has a moral standard higher than Chazal, I think, is an apikores. Some forms of vegetarianism do claim a higher moral standard than Chazal, and that’s much worse than being stupid.