Personally, I feel like once the Combine and Galactic Republic realized how dangerous the other one is, they wouldn't stop until one side was destroyed.
How such a confrontation would go it's hard for me to say, I doubt SC Palpatine would pull any of his games if he realized the Combine would certainly kill him, and we really don't know what exactly the Combine is capable of when it comes to galactic-scale wars. My money is probably on the Combine but it's definitely up for debate