Maybe Ward really didn't understand who or what he was working for, but that was no excuse. That was actually a big part of why Skye never really got SHIELD's whole trust the system thing. She had trouble understanding how people could just blindly follow orders without asking why. She definitely wasn't going to excuse his actions based on him not understanding just who he was working for, though, no matter what his training had taught him to do. Just ding what you were told didn't give you a pass.
"You're working for them, Ward. HYDRA? They're a bunch of Nazi's. That makes you one, too!"
Right now she didn't give a crap why he was working for them. In fact, if it was anything other than actually believing in their cause, that made her respect him less for his actions, not more. If was one thing to fight for something you believed in. It was something completely different to do all those things just because some asshole told you to do them, no matter who that person was.