So may be not bravest choice but not illogical either..

I think the word you're looking for is 'not implausible' . If he really does care for these people as much as his horror at seeing himself killing them shows, logically deciding to do it again and again 100x more just to avoid imprisonment would be pretty contradictory in logical terms, unless he was more concerned about his emotions than the people. It is ultimately a choice between perception and reality, do you perceive yourself killing 3 people, or do you kill hundreds but without the perception? Also there is the question about whether he's really himself after he's reprogrammed.

(In a way, that kinda reminds me of the dilemma of whether transgender people should change their brain gender instead of their bodies. It would make the future life somewhat happier and easier, but also fundamentally change you so much that the present you would be appalled and disgusted with future you. Is the person whose life you are making easier still you? )