It seems as if the Dev. is subconsciously asking forgiveness through the MC to the Patreon Gods. This is not the first platform that this whining technique is used when actual or implied Incest is used. Oh woe is me I don't know what I am doing, oh what have I become. It's intellectually insulting. Man up and accept what you put your name to and stop allowing for a spineless MC.
"Manning up" however has to do with how you deal with stuff happening towards the outside. Nobody can turn their internal conscience on or off at will. And this is internal monologue, he is not telling it, we just see it. And thoughts/regrets/insecurities are a thing people may have even years after a fact, even if they intellectually know that they are not at fault at all. Especially if people around you will act as if you're doing wrong (the specific people don't do it here but society as a whole does). Also by the way, "manning up" is about facing challenges not ignoring them and pretending they do not exist.
So I'd argue that it is realistic that MC has second thoughts and may have them for years to come, maybe for the rest of this life. But as with other realistic stuff the question is "does it serve the story?". After all, a stomach flu is realistic but if it does nothing for the story we don't want 25 lines of the game exploring it in detail. And this will be a matter of taste. You may not want to see this internal dialogue because you'll see the game as an escape and would see no need to explore every consequence of the actions taken (just like we usually don't want to see how many people fall by the wayside seriously harmed in an action movie - blow the evil guy up and we celebrate). You might want to play a character who does not have that kind of second thoughts. Or you might like some insecurity because it may make a character more relatable, also because it may be another story about overcoming an obstacle - this time internal.
And personally, while I wouldn't mind having it turned down by 10% or so, and Francis might also show a bit more activity in dealing with the stuff than just pondering about it, I am happy that in some games the character isn't a Marty Stu type "perfect guy" who can do no wrong, who will not be questioned (or if he was the question would clearly be wrong). There's enough of them in other games out there to enjoy, and I do enjoy some of them, but sometimes some variation is welcome to me.
