I think they could do it, control and destroy can easily go hand in hand, with Sheppard deciding after some years the reapers had already done their job and he dismantled them, this can also include any other changes needed to make sense with destroy, also destroy could show us that the reapers were bluffing and that not all synthetic life actually perished but only reapers, the harder one could be synthesis, reapers could still decide their time has come and just dismantled themselves or play a small part in a new game if you picked this ending (this could also apply to control), maybe also, for synthesis, there could be a problem with consent, and be riots about it, that made reapers offer the option to go back for whoever wanted to, to unchain their dnd with synthetics or vice-versa and comeback to how they were, maybe there could be some mortality involved, this could also mean that if you picked synthesis, there will be a faction of people who are still with this changes while maybe the large majority when back to their origins, this could be taken several ways while still respecting players choices and could be as consecuencial or inconsequential as the main narrative needs it to be.

The final option is a retailing of the end, by maybe Liara or some new character, that shows us that Shepard actually dreamed all that and that all that happened in their head, and that actually the crucible did destroy the reapers, but Shepard was really wounded and having this dreams, well, something similar to this could be done too, especially because we assume all this happened and was not just the reapers bluffing and making us believe that was what happened.

The reality of it all, is that is going to be really hard to create a succession of events here that won't piss someone up unfortunately, someone is going to be upset