So this is what I've come up with so far.
What would cause Magneto to willinging join forces with the xmen? What could cause such chaos that they'd have no alternatives? What would cause Xavier to trust Erik? Well since some of the people are going through this 'seige perilous'/ Memory Eater what if Magneto himself were a victim. It would explain why he might suddenly start acting a bit different, and he'd be 'good' for a while before he started remembering things.
The Brotherhood could have been activly going after some mythosy group & their pet Memory eater that had previously attacked some mutants. Or Perhaps the group in question decides the Brotherhood is just getting out of hand and decides to attack them instead. Which might be more likely. The main strong hold is over run, mass chaos occurs, Brotherhood forces fight back but there are great losses and they end up falling back. Before Erik finally falls to the Memory Eater's attack he's able to warn Xavier of it's existance thus the 'They are coming for you next' line is given. While he has issues with Xavier he still doesn't want to see them wiped out either.
Thus with Erik going through a "I don't remember every thing' stage He's less likely to cause major issues and maybe Xavier will think he has a chance to 'reform' Erik and get him working for his cause. This will also allow him to fully believe in the Excelsior / Pro Mutant idea until it gets up off the ground.
Of course Erik will eventually start to remember things and Humanity in all it's wisdom will do plenty of things to piss him off into going back to his bad old ways.
Thougths? Queries? Love it? Hate it? No throwing of tomatos please..