The blood they showed makes me believe Hand (she'll always be Angel from Wing Commander to me!) should really be dead, otherwise they are drastically fucking with us. In that light, it wouldn't make a lot of sense for Ward to go to those lengths just to root out the remainder of Hydra, because they already know that Hydra was successful in a lot of other areas of the world, so it is doubtful he would somehow be able to "strike a blow" that brought them all down. And killing "one of the two highest ranking SHIELD members left" doesn't seem to be worth whatever questionable benefit Ward could have undercover.
Don't get me wrong, I'm sure they can explain how she isn't really dead if they feel like it, but it seems like they went to fairly drastic lengths to show that they were all really dead. I'm hopeful that he really is evil, and he asked to be written out of the show because he can't stand having to do kissy-face scenes with Skye, whom he clearly hates in real life. I don't expect them to go that route, but it would be nice if someone really was a turncoat for a change on a show that isn't 24 or The Following.