Maybe they didn't kill him, because they feared that it wouldn't stop the cracks? If they just kill him, the cracks are still there, but removing him from history (if that's what "the Doctor will be prevented" means) might do the trick.
Killing a Time Lord is a tricky business. Just when you think you have it al sewn up, the little bugger regenerates. And the assorted aliens in the so-called alliance know that all too well.
If you want to kill a Time Lord, you need to do something absolute. Like lock him into his own TARDIS, with no means of escape and cause it to explode. That'd fix him. Of course, you might cause an explosion so great you'd crack the universe...
In which case the alliance effectively
save the Doctor's life by locking him up while the TARDIS explodes. Now there's irony.
The question is who would hate the Doctor so much they'd risk cracking the univers? And I think the answer is the 'Amy's choice'. Add to that the fact that the voice in the TARDIS sounds to me like it's meant to be William Hartnell - and we know that the Doctor's previous selves make an appearance in the finale and I think we're looking at some sort of misguided suicide attempt. What I don't know is
why, or
why he doesn't remember setting it up, but people forgetting things is a definite theme of the series.
The second question is River's timestream: In 'angels', she's imprisoned for having killed the best man she ever met. And that is
after the events of the pandorica opening. In this ep, she's imprisoned (why?)
before the pandorica opens. She herself might have bobbed around time, but her memory should be in a straight line - when she gets the message from Churchie, the pandorica is closed and she doesn't know what's inside.
Then there's the question of how come Auton-Rory apparently has Real-Rory's memories. I don't think we've seen the last of him yet. Personally I hope not: the dynamic of the Doctor's companion having her own proper love-interest was something new (and unlike Mickey who was clearly only a make-do-till-I-meet-someone-better interest).
I'm going to watch it again tonight, in the hope of making out the kitchen sink, which I'm sure put in an appearance somewhere. It's there in all the finales, and this one should be no exception. EXpect more questions later.