To be fair to Equius and his redeeming qualities, he was something of a pacifist. He never hurt the other players and did offer to remove the program from Aradia before she fixed it herself. And like you said, he did find himself at conflict with the hemospectrum, which is a lot from somebody who was raised to uphold that system

His pacifism actually goes beyond that, to all living creatures- He finds Nepeta’s hunt of animals, even to eat, somewhat distasteful, implying he’s a vegetarian. He builds his robots explicitly so he won’t have to harm anything else, which is commendable since he’s kind of freakishly strong and can bruise Arthour just by gently patting him.