Stumbled on this thread by accident and didn't realize anyone else was still asking this question.
Obviously, River blew up the Tardis. The voice we hear in the background "Silence will fall!" is a voice in her head, probably triggering a subliminal command programmed to fire if she ever finds herself alone in the TARDIS with no one supervising her. She was programmed to fly the TARDIS to a location where the Doctor could be expected to be (the night before Amy's wedding, for instance) and then set it to self destruct. The Doctor would then arrive just in time to be blown to bits.
Just like the Lake Silencio thing, the entire plan blew up in their face and took the entire universe with it. The Doctor probably worked this out a while ago, and as usual didn't mention it because he knows there's nothing River can do about it (she doesn't even realize she did it) and it's all in the past anyway.
In general, the Silence are sort of a self-fulfilling doomsday prophecy. Paradoxically, they are a group that is determined to prevent the destruction of the universe, yet their every attempt to do so causes the very destruction they are attempting to prevent. It's like standing nose to nose with a weeping angel and somebody tells you "Don't blink!" instinctively, you blink, and are immediately zapped sixty years into the past. Then you spend the next sixty years thinking about how to prevent your demise, one day you realize you need to help your younger self so you run up behind yourself in a showdown with a weeping angel and yell "Don't blink!" just in time to see yourself zapped into the past.
The Timelords, probably, have ways around that sort of problem with a technique for breaking out of those sorts of causality loops. The Doctor, certainly, excels at this sort of maneuver. The Silence's obsession with the Doctor may reflect their desire to replace the Timelords as the new stewards of time and space in the universe; the fact that they actually suck at it may explain why they never seem to accomplish anything other than getting everyone killed.