(Sketched in my phone during a twelve hours long bus trip, so take it as you will).
(The why: I thought the whole Utah thing was quite well put together, including Eleven's escape, and ditto for Gallifrey Falls/No More, but on in contrast the whole Town called Christmas thing just didn't make sense, even in the kind of sense Doctor Who aims for. This is a half-assed outline of a variation that I like better.)
Trenzalore stays, as well as On the fields of Trenzalore, at the fall of the eleventh, when no living creature can speak falsely or fail to answer, a Question will be asked, a question that must never, ever be answered., and yes, it is the Doctor's name. Also: Trenzalore as a battlefield, the dead TARDIS, etc (some of the most extraordinary images I ever saw in Doctor Who).
Here's where the changes begin: Time Lords keep their "true names" secret, because they use them as passwords for the important stuff (problematic, I know, but you do want a master password, and biometrics don't work after a regeneration). When the Doctor(s) put Gallifrey in stasis, he/they sealed it with their password... their name. He doesn't know "where" it is, but if somebody finds it, they won't be able to unlock it (and potentially unleash the Time Lords again) without the Doctor's name. That's what the Master (of course) is trying to do (he did find Gallifrey, but he never knew the Doctor's name), and that's what the Silence (quite reasonably) want to avoid: they come from a future where the Master succeeded, and the Time Lords overran the universe. The only way they could survive was to make the Time Lords forget they existed (for all we know, they are what humans had to become to survive, which is why they set up their trap on Earth, which they did have some previous knowledge of), and that's how they could steal a time machine and go back to try and stop the whole thing.
Note that this is also the timeline Eleven saw the outcome of when he visited Trenzalore: when the Master unlocked Gallifrey in mid-war, the Gallifreian army went out all ready to wage war upon the Doctor (or at least part of the army), and the Doctor fought them for years (if you want to go all retconny, he has been traveling all over the place in part collecting knowledge and tools he'd need in case he ever had to), until they finally kill him. Hence the rivers of blood, the Doctor as the beast, the dead TARDIS. The Gallifreians escape, etc. This is the main timeline, and it's about to happen again.
What changes? Nothing. The Master gets the Doctor to Trenzalore, sets up the veracity field, makes him say his name. But even when telling the truth, the Doctor lies. Knowing what was coming and guessing the rest, he put Trenzalore inside a pocket universe, and Gallifrey in a pocket universe of that pocket universe. Gallifrey is free, he fights the Time Lords to make it believable... he even dies to make it believable, and also to give the Trenzalore universe time to detach from ours without them noticing it. It's only after the Doctor finally dies that the Time Lords realize they are still trapped, and they launch themselves in a very long between-universes trip to reach ours, which is why they aren't in Trenzalore anymore.
And then... Well. The Doctor is truly out of regenerations, and River is dead, but the Master was left behind by the Time Lord fleet (actually, Gallifrey with a Ugiroth Drive (just made up that name)) to go crazy and die, die, die until he's truly dead. But he knows the Doctor must have had some escape hatch in case he survived or he needed to get somebody else to safety, so he revives the Doctor with one of his regenerations (and the TARDIS with another), in exchange for both of them leaving the Trenzalore pocket. The Doctor isn't keen on letting the Master out, but with the Time Lords going to eventually reach our universe, he needs to get out and start preparing for them again. This time, it'll be in the right (wrong) universe... And he's probably going to need more lives in order to get ready (But should he? He doesn't particularly *want* to; Eleven was already a bit gone, and Twelve... what Eleven did was in a sense worse than what the War Doctor did, and he's certainly in shock. But... there's people to save. But... what costs are there in seeking more lives? What cost did the early Time Lords paid for their regenerations, and will he be able to pay it on his own?)