Messy?... Yeah possibly. But the thing that seems to be lost in that logic is exactly the egos involved here. Bruyneel, Armstrong and Contador all want to win above all else. That is a force that will bind them together more than split them apart. The key is defining what each of them has to win and lose.
Contador wants to win the Tour so badly, he has trained to a fitness level that has almost unprecedented. He also wants it bad enough to get caught making impulsive and senseless tactical decisions. His ego and desire will likely keep him tied to Bruyneel, because it represents expert tactical nuance, and the best opportunity for a repeat victory. Love or hate him, JB can build a pretty compelling Grand Tour program.
Lance has always had more to gain politically by just doing well in the TDF, rather than by winning at someone's expense. He doesn't need the controversy or the win, which is not to say he hasn't been competing for it. His competitive level and profile has brought him a new U.S. sponsor, and a way to be involved in Professional racing, and feed an ego that loves a high profile. He just finished 16th in a flat time trial. I think he is well aware of his competitive mortality, but his future team will be less impact-full if they don't control the TDF. His ego will be best served by becoming a mentor for Contador and maintaining a high profile in competitive cycling through top performing team.
Bruyneel understands better than any of us what potential Contador has. His interests will be best served by keeping Contador in place and happy. And for all of the absurd speculations and press inspired controversy, there is little to support the line of thought that Alberto is unhappy with the team. There has been not one action by a team member to threaten his GC position, and there certainly could have been. A few well documented rookie tactical moves should reinforce with Contador that he is better off with an experienced DS and a powerful team with a budget, a roster, and a profile that Armstong's association can provide.
All that being said; I see a messy fight with Astana over actual team ownership and legal challenges over who is contracted to whom, as well as the controversial return of Vino. So who really knows where this will all end up. Generally all bets are off at transfer time, so we will see where the dust settles. But impetuous reactions aside, why would Contador want to go anywhere?