Paradox is possible, after all, if all creation is wiped out, then there's a paradox right there, because without any Universe, there's no Universe to destroy, no Doctor to lock up etc.
This is what I mean by I hope they don't go Brannon/Braga on us, the whole 'reset button' approach would annoy me greatly.
No, I think this is a love story, and I think the answer, at least for Amy and Rory is that where the cracks are concerned, they are running in the wrong direction, but we shall see.
As for the supernovae, I'm not sure what they were exactly (ignoring the whole physics/speed of light thing) maybe the Doctor has been in the wrong universe all along, maybe the Tardis has finally decided to fix the broken Space/Time Continuum, it could really be anything at this stage.
Remember, as far as these cracks are concerned, the Cybermen never attacked London, the Daleks never attacked Earth etc, that sounds to me like one of those Universes was the 'wrong' one