Is it still considered not just/not compassionate to attack a non-evil beast? Or are beasts/enemies even separated between evil and non-evil anymore? I've noticed that snakes and what not are actually chasing my party now, rather than wandering aimlessly like in U4, so that in combination with other changes like the lack of runes, has got me wondering.

It's fine to kill any hostile creatures as well as fleeing enemies now. Instead of virtues you have a karma system that's mostly lowered from stealing and butchering townspeople.