I understand where your coming from and I do understand the logic behind the decision but for me I don't really have any options when it comes to ME3 ending, I cannot condone the genocide of an entires pieces especially since they are more or less innocent, I cannot become Hitler.
Comparisons to Hitler and whatnot can get a bit squicky around these parts, but I'd really like to address it, because it's really unfitting that any of the decisions made at the end of the game can even be remotely compared to the choices made by the Nazis.
For starters, the deaths of allied synthetics in the series is not an active decision made by the protagonist in and of itself, which is a very important distinction. Shepard did not facilitate their deaths with the actual intent of getting rid of them. After all, if the geth are still alive at this point, obviously the intention was to keep them alive to see the end of the war, and potentially even join the rest of galactic society. Obviously, this all changes once the arbitrary connection to the reapers is established. And on that note, it's the reapers themselves that can make any option pretty much justified. After all, they are a continued threat to anything and everything we know. Even as the Catalyst wastes Shepard's time with its ancient AI-ness, allied forces are still being blown up and vaporized all around him/her, which makes the Catalyst's statement that it controls them all the more frustrating. The only ones in which the protagonist is intentionally eradicating in their entirety are the reapers, and that certainly isn't comparable, since they are an enemy combatant.
Aside from that, each choice presents a serious problem. Like, what the hell is Synthesis anyway? Some weird thing that a machine that thinks liquifying people leads to ascension is pushing it as the optimal solution, and the other is basically something that we've been fighting against for the entire plot. And then to even make these things come to fruition, the protagonist has to commit suicide to do so, and personally, I'd very likely have the audacity to put my own life above that of my enemy. That some of my allies are tied to them would be unfortunate, but my goal first and foremost would be to destroy the enemy and liberate the galaxy from their presence once and for all, and all other considerations would be secondary. Hitler suffered no such dilemma. This isn't accounting for any person's crazy delusions at the time, but I certainly wouldn't indulge that.
That said, I understand the reasons why some refuse to ever consider destroying the reapers, but I defy that this decision is in any way comparable to the extermination of millions of people in the death camps.