Aside from some nitpicks in ThoseDeafMutes arguments that probably aren't worth, well, nitpicking, I agree with just about everything everybody has said regarding this "Reaper logic" discussion.
At the bare bare minimum, I think the fact that such a discussion is possible pretty much destroys ANY chance of credibility for the xzibit meme, which was essentially my only point to start with.
They didn't directly mention a singularity, but an existential threat to organic life is one of the popular proposed endgames, so that's what I thought of as soon as I heard Reaper logic for the first time. Maybe projecting this concept onto the situation helped me not hate it as much.
The ending choices (well, not synthesis; that one's utter nonsense) give some options, if you don't believe the Catalyst. If we think their logic is crap, and we think they're wrong, we have the option to say, "Okay, cool, I guess I kind of see what you're saying, but instead of being so rigid with this genocidal mandate, let's just monitor everything, and use the Reapers to make sure things go smoothly." It can be argued that there's a ton of hubris in taking this path, but it's an option. Then of course the option to just throw everything away and leave it to nature is there as well.
In terms of scifi villain motivations, the Reaper logic worked okay enough for me, personally.