I don't think, that Bungie or MS will want to break up. They both make to much money off each other.
If that happened, it would be the greatest thing ever.
Since the Halo series is over it's probably not worth the amount of money Microsoft has been paying up until this point to keep them as a first-party developer anyway. I say if it's ever going to happen, now would be a good time.
Psht, knowing MS and how much money Halo is worth... there wont be another sequel, instead they'll start working on prequels since the trilogy is over... like Star Wars.
I think that it's a rumor and only a rumor. Theres no way Bungie would leave MS.
They will probably start a new mega-funded series which they will make several parts of and then a new one or go back for a new Halo game. The blizzard story in a way.