Earth and Mars were already 'Allies'....
...Who had been steadily heading towards a massive brawl in the system for decades. But Prior to the
Canterbury and then
Donnager incidents, things were tense but manageable.
Now? With a confirmed hostile threat to all of humanity that already has a butchers bill of 30 to 45 Billion already on its plate, you better believe that alone will draw Earth and Mars close. The Belt wont believe it until Cylon ships start showing up in system and blowing up ships.
And the Cylons are most definitely going to be hostile. Their idea of peace is enslaving the Human race. That isn't going to go well with Earth and Mars. And the Cylons will definitely go for the creepy Pseudo-incest vibe with Earth they did with the Colonials.
Cylons: "You're our parents. You're responsible for us. Lets bang!!!"
Earth/Mars: "AIs who believe their humans, think that they're our children and want also want to have sex. Hard pass, No!"
Belters: "Pashang ya, lets bang!!!"
The War, depending on when it happens. And it will happen. Could go either way. Earth and Mars are going to have to throw their fleet doctrines out and build a new one. As it is now, Earths ships have superior range in terms of weapons and firepower as Railguns are just better than Colonial Electro-thermal Kinetic canons. So I figure the first few battles will go decisively in Earth/Mars favor as the Colonials are simply not prepared for the kind of weapons they have.
The Cylons will then shift tactics. Where is the Cylon fleet? Everywhere the Earth/Mars fleet isn't. FTL gives them a massive strategic advantage in terms of tactical and strategic mobility. Until Earth and Mars can can compete on an equal or near equal footing, then the Cylons will set the pace and tone of the war as their FTL gives them the initiative.
This is going to be a very long, very bloody war that could see billions dead. And I don't see this stopping Proto-molecule research. Infact, I see it pushing it into high gear. Obviously it'll change how Protogen goes about doing it. There wont be an Eros/Venus mass experimentation situation for example. I forsee Proto-Molecule research being much more focused and tightly controlled and focused on war time goals.
Ultimately I see Humanity winning, but it'll be a hard fought victory.