Averted in Red vs. Blue: Reconstruction - the Chairman of the Oversight Committee implies that their government has a series of moral guidelines for dealing with AIs. After evidence that the Director of Project Freelancer tortured an AI in his experiments comes to light, the government decides to create a set of strict morality protocols.
Subverted: In the Epilogue, the Director justifies his actions, implying that the torture he inflicted on the Alpha AI was acceptable because it was created based on his own mind - he was essentially torturing himself.
Of course, even if the main characters knew this, it's highly unlikely they'd be inclined to forgive him. Wash, Meta, and Epsilon certainly haven't.
And odds are same with the main Halo universe which RvB is based on.
Averted in Freeman's Mind. Freeman has no problem killing anything trying to kill him, alien or human.