I dont see how they can just leave then.
Because you can buy a company but you cannot buy people. At some point the contracts of the employees to continue working there are going to run out, and they are then free to leave, leaving Microsoft with a company called Bungie which has none of the Bungie employees. What is being rumoured is that they are being allowed to keep their name because it's not much use to Microsoft if they no longer have any of the developers. In return for which, I guess Bungie are giving up what few ( if any ) rights they had left to the Halo IP.