I know that it's pretty unlikely... but I want this to be building up to the Marines no longer being a major threat post-Egghead and we get an Akainu vs. Imu fight.
Now that the true stakes are being unveiled and the threat of the entire world being destroyed, I don't think Akainu is the kind of guy who would roll with that and continue serving the World Government. He's
already had some friction with the Five Elders, and in
his fight with Kuma he comments on Kuma being a "puppet with no mind or will left..." which I believe also symbollically connects with Akainu feeling like a useless puppet of the World Nobles.
If he's given a good reason, I believe he'd turn on the World Nobles - he hasn't expressed the same kind of fanaticism that Aramaki has towards them.
He may well storm Mary Geoise (which is where he's at currently anyway) and go to confront the Five Elders, unaware that they've teleported themselves to Egghead, and he may come face-to-face with Imu instead who will kill an insubordinate Fleet Admiral since he no longer needs him if he has a weapon like the Mother Flame.
I also think Fujitora & Kizaru will defect from the Marines, and Aramaki will remain loyal to them.
The main antagonists for One Piece following this will no longer be the Marines themselves, but the Holy Knights (+ Aramaki) and the Blackbeard Pirates.