First thing my hurty brain comes up with? Death brings them back. Seeing as how he's the one complaining about how they screw up the natural order, wouldn't it just be so fitting that without Sam and Dean, the "natural order" is even MORE screwed up, and Death decides that having Sam and Dean around, troublesome though they are, is better than the alternative.

Or, it could be that Raphael wipes them out of existence, and Cas brings them back.

My brain, it hurts.