IN Real Life, if Michael wins and negotiate an acceptable peace with humans, he will rule, for a while, While humans asses his government. Bear in mind that Abigor can be controlled easily because he is several order of magitude more ignorant than Michael, and less slimy (odd, putting the demon in the better half of a dirtyness comparison
), but Michael can't be left to rule as he pleases, although he won't attack humans in a couple centuries more. If he wins, and doesn't negotiate, is NukeEmAll followed by CrapSackWorld and BittersweetEnding. That's not happening. Then again, this isn't Real Life, so...
However, possibilities are far more interesting should he lose. If he defeats Yahwe, and gets killed in the process, the nakama are suddenly leaderless, and Lemuel can take over with HEAVY aid of the humans. Social and political tensions in that power distribution could make good material for the third book. If Yahwe defeats him, and the nakama (useless in this scenario for the most part), maybe Yahweh would be very weak and easy to finish by either Lemuel, Jesus, the humans or the first child that pass through the gates. I can see a dying Yahweh being ripped apart by the Elders, for example. Then he can be treated either as a martyr or the resistance or as the brilliant politician and plotter he was, depending on who writes the history.
One thing is sure, Lemuel is not going to kill Michael (he knows Michael is far more powerful than him. He can antagonize, but not kill. Besides, humans are not going to let him) nor is he going to forgive him. A couple punches and Michael letting him, while his friends control Lemuel and the humans watch is an acceptable outcome.
So Michael ruling is ultimately a problem of how much punishment the author thinks Michael deserves. But in this case, the best way for Michael would be to follow the words of Harvey Dent and DIE a hero's death. Otherwise, is not going to be pretty for him if the truth gets out. Which WILL, eventually.