Flamewielder wrote...
Any attempt a morally judging the Reapers from a "universal" perspective is doomed to fail. Would humans consider Reapers "evil"? Some will, according to their own perspective. Do the Reapers feel any qualm about consuming a resource to survive and multiply? No. Do humans object to being liquefied? Of course I would! I like my individuality just fine, thank you, however painless you might be able to make it... 
Out of all the crazy in this thread - and there's plenty of it to go around (I'm looking at you, TC)- your unique brand of moral nihilism wins out. Your problem is you're treating the Reapers like they were dropped into the universe, totally innocent and uncontrolling of their nature. I might be able to sympathize, or at the very least understand, your position if the Reapers were wholly organic beings - their nature an unpredictable consequence of their particular chaotic evolution.
But they're not. They're constructs - meaning, their creators (and I'm coming more and more to the belief that their creators are the "original" Reapers, voluntarily sacrificed in a vain attempt at immortality) made them in this way, to be dependent on organic matter and to systematically harvest sentient beings. If I create a robot that I program to kill everything it sees, I am evil in its creation, yes, but the robot does not cease to be evil in its own right, as it was born of evil intentions.
Moreover, if my theory about what the Reapers are is correct, we don't even have THAT problem. They're both the creator AND the robot, and thus guilty either way. The Reapers are not intended to be, AT ALL, an enemy that is supposed to be sympathetic or have any depth to them. They're ruthless, arrogant, EVIL, killing machines. Literally. Your arguments to try and compare their relationship to us akin to our relationship to fish might hold some weight with me if you could produce the slightest evidence that the same kind of cognitive superiority over fish which we enjoy is true of them in relation to us.
I would think, by virtue of the fact we had a conversation with a Reaper, such a divide is nonexistent. Because trust me, the day I can communicate with a fish is the day I stop eating them. Good vs. Evil is not nearly as subjective as you're claiming.
Flamewielder wrote...
Destroying the Reapers won't feel like a "righteous smitin' of evil" to me, but rather like a very hard and unpleasant necessary extermination. And that's from a player who has trouble playing anything but uber-paragons...
And this is ridiculous and contradictory. I won't even bother to say, "See Above" for why it SHOULD in fact feel like a smiting of evil, but even under your own logic - you should feel no regret, just as you argue the Reapers should feel none. If it's all merely a struggle for survival, with no moral element, you have no reason to hesitate.