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I don't think this situation actually has a huge amount to do with alignment (at our table we use alignment as a fairly soft parameter) but it does have a lot to say about reading your table and your players and making sure that the situations involved remain fun.
I long ago stopped including certain situations in my Pathfinder games because they are just not fun for me or my group of players.
In my games violence is described cinematically but only in an Indiana Jones-Star Wars way, not a Quentin Tarantino or Raging Bull sort of way. We don't kill children, even the children of monsters. (My world has a mysterious lack of younglings...) I regularly GM-fiat situations where fun action might turn into creepy weirdness or animal cruelty or whatever. ("After his master dies, the ape seems to fade away into the shadows...")
I also don't allow creepy sexual or sexist behavior at my table - an occasional double entendre or flirty joke, fine, but my Pathfinder game is not the place to act out fantasies of sexual prowess or control. Why? Because for most of my players it's not fun.
Finally, I don't allow PC-on-PC violence or aggression ("No, rogue, you can't steal the fighter's stuff...) except in very rare situations where a PC is controlled by an NPC somehow. Again, why? Because in my experience at the game table it winds up never, ever being fun.
I mention all these examples not because I think they're worth adopting, but because I think every GM should learn pretty quickly to read his or her own comfort level and the mood of the table.
If some of your players think killing mountain gorillas or apes is disgusting, find a way to leave that out of your game.
BTW, enforcing this kind of "standards and practices" at the table is the one area where I very comfortably "railroad" players. Just because you have a particular alignment or class doesn't mean you can creep everybody out, disrupt the story, or kill the fun.
But the same also goes for the GM. Even if I think a situation might be cool or edgy, if I think it's wrong for a particular group of players, I rewrite it or soften the edges a bit.