Pfft, no killing's easy. No alerts is the hard shit.
The first bit is what's hard, because you don't have access to your tranq guns. You have to actually wait for the guards to pass through instead of knocking them the hell unconscious. As far as the boss fights go, I did then all with no kills on my first runthrough, I can certainly do it again.
you had trouble on the second boss? Seriously, I just went to the roof and used my Mosin Nagant, it was over pretty quick. She never really hit me. Hell, what I'm worried about is that sequence leading up to it. Beast the first took me longer than beast the second.