I know.. I remember the beginning and the first time you kill someone and the char is all "omg I just did that.. omg. omg.." Then brutally murders people and animals less than 20 minutes later without any thought. It definitely threw things off.
Haha yes, TotalBiscuit mentioned this and coined the term "ludonarrative dissonance" in his Tomb Raider video, another game where you are a normal person sissy and turn psychotic murderer in twenty seconds without anyone even taking notice.
Actually I think it's very much tied in to what the norms of single player FPS gameplay are. Games where you aren't one person fighting a whole army of AI dumbdumbs are in fact extremely rare. This is incredibly unrealistic too. Ten years ago all the characters we had were cliche badass dudebro types, so it wasn't really a problem to see them kill thousands of people. But now that we have characters supposed to have emotions it doesn't make sense anymore. Also this is even apparent in parts of the game that are "pseudo-gameplay" such as QTEs. Very frequently, this type of game sort of "enters QTE mode" in order to force some negative event to happen, such as you getting ambushed and captured, because that would be impossible within actual gameplay. Interestingly, FC3 did treat the subject a little bit better than TR by at least acknowledging the fact that the "hero" became a mass murderer.
It seems the designers either failed to understand the issue or couldn't find a satisfying solution in gameplay. I think it could be possible to make realistic gun fights with very few enemies interesting, that would at least reduce the dissonance.