About time we got something of substance! Now some speculation. The first question is: why blow up a library? The answer: to destroy obscure historical evidence of something that didn't make it into the digital archive (an escaped sleeper ship, maybe...). Why assassinate fleet command? Because they have top secret knowledge about a facility housing obscure left-overs from history.
The good news: Harrison probably isn't Khan. The bad news: I think those who believe this is a set-up for a third movie *with* Khan might be on to something.