Perhaps now Dean won't be reluctant to explain exactly what was going on, since he presumably wasn't being forthcoming to keep Lisa from freaking out and breaking things off with him. That way, still broken up, but Lisa and Ben won't be left thinking he'd be violent toward a kid like that under normal circumstances.
Well, since what we have now is a shell of Sam, and his soul is elsewhere... I'm assuming his soul is still in Hell as Lucifer's and Michael's chewtoy, and has been for the entire year plus now. The body returned but the soul remained behind to continue being tormented.
I doubt that. For one, anything they could do to get Sam's soul back out of the cage now would likely risk releasing the archangels and starting the whole apocalyptic mess over again. I think wherever Sam is, it's outside the cage. I would hope that while God was recreating Castiel (and resurrecting Bobby via him) in the aftermath, he also transmigrated Sam and Adam's souls into Heaven. Although, this being SPN it was probably some sucky traumatic experience instead...