It's been stated a couple of times that "The End" is not considered in-continuity. Tom Brevoort specifically mentioned this around the time that the Thanos series was announced, as people were very curious how the events of that mini-series would affect the main character (Thanos), as he was left dead at the end of... well, "The End."
Thanos references several of the events in "The End", however, which would lead one to believe it is in continuity. Again, though, Tom B. said it wasn't necessarily the case- that in the "proper" Marvel universe, events similar but not exactly like those that took place in "The End" might have occurred to the "mainstream" Thanos.
Very confusing, yes.
At any rate, I wouldn't put money on any deaths in the MU ever being permanent- even with Joe Quesada's "no resurrections" "rule" in place. Magneto's already come back, seemingly, twice since that edict was first laid down; Colossus is back; one of the characters who is meeting their demise in Avengers Disassembled is supposed to be coming back (Joe said the idea to resurrect them was the best proposal he'd ever seen).
Not to mention what may or may not happen *after* Joe Q. is replaced as Editor-in-Chief someday. (Not that I think that's likely to happen soon, but I'm pretty sure he won't be there forever.)