Yeah, they just tried to handwave away the moral implications of forcing synthesis on every living being in the galaxy with that one. "It can't work if the people aren't ready, but it will work so the people must be ready."
It wouldn't solve a damn thing anyway. People may accept the new fusion, but that doesn't mean it will change what their priorities will be on Monday. Aria will still slaughter anyone and everyone to get back Omega (though, I'm betting we'll get to see that pre-epilogue as DLC). So what if she glows green and has a new appreciation for the Geth? Synthesis just means that organic and synthetic can develop new ways of killing each other at the same rate. It doesn't change anything, aside from obsoleting night lights.