Personally, I think it'll be #3. They'll canonize 'destroy'. In terms of narrative it would have the least impact and give them the best platform to move forward in terms of keeping what they had in ME1-ME3. They'd lose the Geth, and they'd lose EDI, but beyond that, not much difference.
Of course they could also pull a minor recont. that keeps the Geth and EDI in play if they want to.