Issue: I simply refuse to use the stun gun on any robot in Delta

[grrrz]

the thing is you're SUPPOSED to feel bad, that kind of the whole point. but this is a story. you're not Simon, even if you make a few decision for him, everything is already set in motion. this conversation is totally surreal.
on this note

Spoiler below!

I was deeply affected by the choice to kill Simon 2, and decided to proceed, thinking it would be too horrific to wake up and discover he was left behind (and that's exactly how you live the end of the game). but maybe I was wrong. same goes for a robot underwater whose totally stuck.
But for the women at the end, there was no dillemma, she lived in suffering and asks you to kill her, you do it at the press of a button, leaving her in her suffering would have been the cruel choice.