Cause here's the thing. The folks in Atlantis are at war. Not a war for land, or for political changes, or even from freedom from oppression like with the Goa'uld. They're at war because the alternative is death and, if the enemy is smart enough, the death of every person on Earth. Yes, in a way we instigated it, because we can never leave well enough alone, but the situation being what it is the only thing that Sheppard and the others can do is fight back.
And yet there's all this aghastedness over the fact that (a) John would order Rodney to blow up the camp and that (b) Rodney would do it without a (c) poignant "woe is me" moment. I don't get it.
If the whole experiment with Michael had taught us nothing by that point, it was that even though it might look human, and might sometimes act human, at the very core of the matter it's still a Wraith -- possibly the same way that John, even effected by the Wraith DNA from the retrovirus that made him all buggy, still retained his essential Johnness. The Wraith that had not reverted or remembered anything were going to be eaten by those on the incoming Hive ship, and the rest of them would have been able to share the information that Atlantis still exists... as well as whatever other information that Michael, who's even more pissed off now, would have been able to share.
Of course, this may have still happened. We don't know how many on the planet were killed and how many were picked up by the Hive after our Hive was destroyed. And in either case, I'm sure Michael is still alive and I'm sure he'll be able to make his own way somehow. Because I have faith they're going to want to bring him back eventually.
This whole thing is a big sticky ethical/moral issue, yes. The idea of the retrovirus started out as this cure-all, this gift from above, but in practicality it didn't work. Would it have been kinder, in the long run, to just kill Michael once they had him back on Atlantis? He did ask for it. But they tried to take the high road, tried to give some form of redemption another chance. Should they have just vented all the transformed Wraith into space rather than set them up on a planet? It would have been easier. But they clung, perhaps naively, to the idea of a cure-all, an easy answer that would justify everything else. And it didn't work.
There's all this moral outrage in fandom over them killing the transformed Wraith by (first trying to nuke them and then) blasting them from orbit, but unless the retrovirus had worked, they were all marked for death anyway. Why? Because they're the enemy, and this is a war.