Depends on how you interpret it, but to me "synthesis" is by far the most sinister of the three options. In my mind, that ending means that the entire galaxy is homogenised into a single collective consciousness, totally wiping out any individuality. That maybe EDI's voice, but it's not her speaking, it's the catalyst.
That was my second thought at least. My first impression was much more horrific. Remember the "green" version of that scene with the human marine fighting off the husk? When the wave hit, for a second there I had the horrifying thought that it had suddenly regained it's former identity...
As for the space magic...yeah, that's just bad story telling no matter which way you cut it--which is why I picked destroy as at least it makes some sense. I suspect they had these different endings in mind but couldn't/wouldn't take the time to come up for an organic way to weave them unto the narrative and instead resorted to a very literal DEUS EX machina (see what I did there?