This is according to Patrick Fortier, who talked a little bit about this in the latest issue of OXM. It seems that you can actually go completely stealthy and non lethal, even with the bosses. Conversations will give you “a different means of dealing” with the situation at hand.
Narrative director Mary DeMarle also echoed these comments, saying, “For Human Revolution, because of the way we designed it, bosses always died in the cutscenes. You had no choice. But we rectified that in the Missing Link DLC, and we’ve rectified it in this game.”
Of course Eidos Montreal have already confirmed that the stealth option for bosses, which was present in the original Deus Ex, would be returning.