Actually, if Shirou isn't actively fighting against the Sekirei Plan, MBI would probably support him against the Clock Tower. Minaka canonically wants to be part of the family, but Takami won't let him, and he wants the Game to continue. If Shirou is as major a player as Minato (and it certainly seems that way), his removal by a party not involved in the game would be disruptive. Plus, if Minaka still wants to be a part of the family, it would probably seem like a good way in: Shirou and his Sekirei are under attack by whoever CT sends, when who comes to the rescue but the Disciplinary Squad.
Personally, I want to know what happened with Rin and Saber, and if they're going to show up. It could be a battle of tsunderes between Rin and Tsukiumi! And I can't help but think Saber would get along well with Miya. And Saber Alter with Karasuba.
Now, a question I hope someone can answer: at some point in UBW did Shirou see Rule Breaker? If he did, I wonder if it could break a contract between Sekirei and Ashikabi.