For me it comes down to the right of sapient life to self determinism. With both the control and synthesis endings you're essentially imposing your will on the entire galaxy, either by self-apotheosis or fundamentally changing the fabric of their existence (which I still don't fully understand on a practical level.)
The destroy ending means that for better or worse, the surviving races will be in charge of their own destiny and with luck, the pattern AI patricide is broken. Of course that would be easier if the Geth & EDI weren't killed alongside the reapers, which I still think was bogus and highly contrived. I my head canon I like to think that they were only knocked offline and could easily be repaired after some time.