Maybe it's just this type of game or maybe it's because this game is just done so well, but as I'm playing I have to say that many a time I feel a hint of sadness when I kill some of these creatures in the game. For example the battle with the big Ogre. I felt like such a dick with how you destroy him, or when you ride a creature and then have no choice but to choke it to death when you are done with it.  I'm thinking this game is just done so well that even the enemies seem to have a feeling of life in them, not just random moving things to destroy. 
 
Does anyone else feel this way? I have heard the same for Shadow of the Colossus, how does the feeling compare to that game, I've never played it.

Considering that even in narration that you have Zobek/Patrick Stewart saying how stone-cold of a killer Gabriel is slowly becoming in his lust for revenge to bring back Marie, I don't think remorse is much of an issue in character. Also, I'm sure if you were to just let them go, they'd have no problem smashing your head in.
 
Shadow of the Colossus was similar in fiction - the character's goal and devotion for cause outweighed the care for any sort of remorse.

I get what you're saying about the various beasts that you mount and ride around, only to later choke them out.  Definitely a testament to how well the game is done.