The "cost" of turning the MC into more of a cold-blooded killer type is baked into the system itself - it denies players access to new recruits, events that require those recruits, and the unique abilities those recruits had.
As for the shift itself, there's a few prongs.
The first, and most obvious, is that if I didn't allow players the option to kill during war then I'd get complaints. Especially given some of the people you'll be going up against in time (Tom, The Chief, Morgana, etc.)
The second is that it marks a noticeable shift in the MC's attitude that - coincidentally - occurs at the same time as he becomes corrupted with the Beast's essence. Wow, that's certainly a huge coincidence! Anyway...
The third is that I always like to offer player choice and agency when I can. These opportunities are limited, as I'm a solo dev on a weekly release schedule, but in cases like this where the "time investment" is two renders and a paragraph of text, I figured I could add it with no issues.
The fourth is that honestly, from MC's perspective, killing certain people may quite honestly be the smartest move. Let's say you fight and beat the Chief... your choices are to imprison him forever (not ideal for numerous reasons, including drain on supplies, motivating the Org to focus attacks on the Manor rather than their currently split focus, and giving the Chief a chance to escape), or exile... which, I mean, he'd just come back. You could try breaking him but I think most people would rather not ;) So killing in that case makes the most logical sense to a lot of people. This is war, after all.
(Also, it should be noted that the execution after breaking the girl is performed by the MC, not by anyone else. MC's keeping that one quiet. "Oh, I exiled her" would probably be his go-to if questioned.)
Anyhoo, just thought I'd clarify the decision making process behind the "execute" option. And if it doesn't fit your concept of the MC, you can completely ignore it. It will never be an enforced option :)