Triple H doesn't need to have been in on it all along. Since the start I've been saying it would be more natural and believable if he really was innocent through all of this, but just gets pushed too far by Punk and ends up snapping/turning.
Even after all this, if Punk keeps mistrusting Triple H, as Triple H has bigger worries like why Johnny Ace tried to screw him, and his best friend continually making his life harder, eventually Triple H cracks under the pressure and goes all Mr. McMahon on their asses.
All these people are making his life/job hell, after he tried to be a good boss, so what does he do? Turns enemies into friends to take out the real pain in his ass who started all of it, Punk. Ace is the ultimate yes man, all Hunter has to do is pay him a little more and make it clear who he works for. Miz and Truth would settle down and join for the chance of more opportunities that would come with being aligned with the conspiracy. Nash and Hunter decide it's stupid to fight when they can work together to screw everyone else and watch eachothers backs just like the Kliq did good old days.
This leaves the two people involved who he wouldn't be able to buy off or control. Cena and Punk. Survivor Series we get Cena, Rock, Air Boom, and (who cares) against Del Rio and a bunch of corporate controlled heels like Awesome Truth and 2 other stooges. Then you get Team Punk (Punk, KoW, Colt) vs. Team HHH (HHH, Nash, maybe Waltman, and some one else HHH was bought the loyalty of).
December PPV, Triple H beats Cena for the title, meanwhile Punk is told he'll never get another shot as long as Triple H is in charge... unless he wins the Rumble. Punk wins, WM main event = HHH v Punk.