Of course, how the geth even got themselves into their situation in the first place is a complete asspull. It doesn't matter what weapon they have, when you outnumber your enemy 10000-1, you have options other than waiting until they've pushed you back onto a single planet and then accepting a faustian bargin from godlike beings or dying. Why the hell didn't they just retreat and regroup in the first place when they realized the enemy brought a nuke to a knife fight, instead of just standing around for weeks and letting their vast planetary empire of multiple billions of platforms and trillions of programs get flattened by a comparatively tiny enemy force, with a population quite a bit less than modern day New York City or Shanghai in a single centralized fleet?
Also the Quarians were on the offensive, while the Geth were tied down defending Rannoch. That should mean that the Quarians control the Mass Effect relay and would be able to retreat if they lose at Rannoch. They might sacrifice part of their fleet to allow others to escape, similar to what both Admirals Hackett and Lindholm were forced to do with Alliance ships. During the initial Reaper attack on the Alliance Hackett had to sacrifice the entire 2nd fleet in a holding action to allow the rest of his fleet to retreat through the Arcturus relay. Admiral Lindholm, who was in command of the 1st Fleet defending the Sol System, did the same with a portion of her fleet to allow the rest to retreat through the Charon relay. Why couldn't the Quarians do something similar at Rannoch, if they lose? Instead of the Quarians being annihilated perhaps just Han Gerrel and a half of the heavy fleet should have been lost, or something along those lines.
The Geth on the other hand, being so spread out throughout the entirety of Quarian space, should be in no danger of complete annihilation even if the Quarians managed to inflict a Cannae on the Geth at Rannoch and destroy nearly every server, ship, and platform in system.
If we ever get a sequel set in Council space I kind of hope that is the route Bioware goes. Instead of trying to account for factions that could be annihilated, have them both survive no matter the Rannoch outcome, and just have Shepard's decision there affect whether the planet is controled solely by the Geth, soley by the Quarians, or if peace was achieved shared by Quarians and Geth who've effectively merged into a single faction. (like the Hanar & the Drell)