I really don't think that Angel could possibly do that. If he truly wants to atone for his part in the whole Twilight thing, and he most definitely DID have a part in it, Twilight wasn't pulling his strings all of the time, it's going to have to involve some sort of positive service, not self imposed brow beating and brooding. I mentioned the Labors of Hercules before, and I think that something along those lines would be very appropriate in this case. Angel spent a hundred years in hell after attempting Acathla, and as far as we know, all that he did there was survive. Atoning for attempting to destroy the entire universe should AT THE VERY LEAST require him to do that much and more.
It's not like I'm saying that we write him out of the story line for most of Season 9. We all know that time passes differently in other dimensions. He could be tried and sentenanced in Season 9, Issue #1, spend four or five centuries in some hell, performing monumental tasks for the good of whoever inhabits the place, then be back in the Buffyverse, all safe, happy, and atoned, no later than Issue#4.
Just think. Angel actually has the opportunity here to do what no other Buffyverse regular ever has: to PAY THE PRICE FOR WHAT HE DID, either willingly or as Twilight's dupe. It could mark the dawning of a whole new day in the Buffyverse. We could call it the "If You Do The Crime, You're Gonna Do The Time" law, and apply it indiscriminately from now on.