Ironically MEA may have made it possible for us to go back to the milky way without having on of the

Not necessarily. It is never confirmed that the Quarians go extinct if you side with the Geth. It was suggested that it might be the outcome during the game, but that doesn't actually occur during it. 

It also doesn't make sense. One battle should neither result in the Quarians going extinct or the Geth being destroyed. The Geth were housed on servers spread throughout Quarian space so losing Rannoch should not be catastrophic, particularly considering it was said that they barely even occupied the planet. There also would be no reason why some of the Migrant Fleet couldn't retreat through the relay following a defeat at Rannoch. Multiple fleets were able to do just that in the wake of defeats by the Reapers, an enemy many times more powerful than the Geth. It would make more sense for the Quarians to just be greatly reduced in number, sacrificing ships to buy time for others to flee through the relay.

The bigger issue would be that the Geth should be destroyed entirely if a sequel is based on Destroy. The Catalyst's dialogue in the Extended Cut however provides an opening for a hand wave. He notes that anything destroyed by the Crucible can be rebuilt, and in response to a question about how the device would affect Synthetics. An easy solution would be to have the Geth rebuilt post-Destroy by the more pro-synthetic Quarians (like Koris). To have player choices still matter they could have rebuilt Geth more suspicious of outsiders and isolationist, while Geth that were never destroyed are fully integrated with the Quarians as a single faction sharing planets. All of that could be handled with codex entries and some differences in the occasional bit of dialogue.

It would mean that Rannoch can't be visited, but that's not really an issue.

Considering how badly they ruined the Milky Way regardless of what ending you picked that may be the only and the best way of doing it.  I guess we will see what happens once they ruin Andromeda.