I was thinking about this, as I did this mission yesterday.
Another way to frame this issue is with how can the Geth ultimately be made a non-issue for organic life?
If Legion is to be believed regarding the conversation with Shepard about the Geth building the mega-structure, that very well could be a Dyson Sphere or something similar, then rewriting the Geth might actually be a better option in the long run.
I argue this because the greatest threat that the Geth provide are using their Mobile Platforms (Troopers, Snipers, Juggernauts, Hunters, Destroyers and Primes) and using their autonomous servants (various drones, Geth Armatures, Colossus, maybe Hoppers, and maybe their Dropships).
So, in theory, without the Heretic Geth, because of rewrite, there should be no more Geth controlled mobile platforms to get in the way of Shepard. The only concern would then be knowing how the other Geth units actually work.
Geth are only software after all right?