There is never a civil war if one side has 90% of the support. A civil war is between prominent sides, not one giant side beating the other small side with a warhammer.

You get mad at Rogue for him BSing, and yet you do it all the time.

Supremes cancel out magic the closer they are to it; 
Supremes have very large ships;
Supremes can call on help from people that do not like the Equestrians, in favor of a much more agreeable Equestrian reform;
Supremes individually are more powerful;
Supremes are smarter, since you're not doing a great job. The Supremes counteract Equestrian magic, and Equestrians rely on magic for shields. Following them into their new Galactic-Center den would mean your crews falling ill and dead within minutes.

While in terms of brute force, the Supremes aren't more powerful than the Equestrians. In terms of using stuff better, there is a good chance that they are.