No, it makes them logical. It makes them realists.
It makes them mass murderers and war criminals. Last I checked, we punish war criminals even if they had "good" intentions.
How'd those tactics turn out for the Protheans again? With their extinction minus one jerk of a soldier, I believe.
Sure it is. An example: let's say you can actually stop the asteroid from colliding with the Alpha Relay, sparing the 300,000 people in that system, but in doing so, the entire galaxy gets overrun by the reapers in a matter of days, seeing a swift end to all of galactic civilization. Would you still stop the asteroid, and accept total extinction over the loss of the Bahak system? That doesn't seem better than anything, really. What good is being "better" than the reapers if everyone is dead?
Yes, I would still stop the asteroid.
In a real world sense, I have no idea how the war will turn out. None of us do. So there is no guarantee of this inevitable loss if they aren't slowed down. At least no more than if we get a few more months. It would also gain us the support of the Batarians, at least in the "the enemy of my enemy is my friend" sense. So the chance to gain an ally over no discernible loss. That's a bargain.
In a metagame sense, we know that sacrifice did absolutely nothing. In fact, it harmed us more than helped since it gave the Reapers months to build up their forces while eliminating a large chunk of a potential ally of our's fighting force.
The obvious irony here is that the whole idea of sparing everyone no matter what can simply end in you being punished anyway. A smaller example: Rana Thanoptis. This fool gets in league with Saren and could very well be indoctrinated, so I shot her. It's the same reason why I didn't release any of the salarians being held on Virmire either, not even the coherent one. They're all a potential liability, so they all stay behind. And it seems that sparing Thanoptis actually has a negative effect, since in sparing her, several more lives were ended.
So we should kill anyone who might pose a threat? In that case, the Reapers would come to a galaxy devoid of life since everyone can pose a risk.
That said, I wouldn't have let Rana go free either since she could be indoctrinated. There are options between let free and kill, though the game limits you to those two.