*snip*
I don't think that quite holds up. If a part of the story of the game was "you have to get your hands dirty, sometimes. Death is unavoidable." whatever, then yeah, you'd have a point. Even a pacifist must be challenged in their views.
But, see, that's not really the case. The game touts choice in many styles of play, including a complete pacifist run, and yet we're just dumped in a room with a guy wielding a rocket launcher and chain gun. We're given absolutely no background on the boss characters, they're just grunts who are locked in the same room as you who fire on sight. Take them out of the game, and you lose very little in terms of story, gameplay, etc...
If you went through the game as combat, you'd have no trouble going through the bosses because that's exactly what they were designed for, straight up combat. There are few, if any, situations where going in guns blazing would be difficult as it's just another way to play it.
Overall, though, they just feel out of place. There's no way to beat the bosses except disposing lead in them. You can't hack turrets to be on your side, you can't incapacitate (not kill) him with gas grenades, you can't be sneak up behind him and pop some caps in him. He tosses grenades left and right and unloads his machine gun in your face. It's just not that great of a boss fight, at least in my opinion. If it was really "adapt and survive", we'd be able to adapt to the situation no matter our initial play style and solve the situation our way.