As I think I've said many times now, I didn't mind that I ended up sacrificing the Geth and EDI. I do mind how artificially contrived the scenario was as presented. A wave of energy destroying AI's that have Reaper code makes about as much sense as one that kills anyone that's thinking about the colour red, or speaks Italian.
They just decided that the most logical choice (destroy) be an organics vs. synthetics thing. Odd as it sounds, I would've been happier if the consequences of "destroy" were wiping out Earth and anyone in orbit too slow to get out of the way.