I let him live. Always let him live in any of my worldstates I create (unless I'm going uber-evil-kill-all-things)
Why?
2 reasons, mainly. Yes, he is responsible for the Fifth Blight by performing a ritual on an Old God. He did the ritual however in an (albeit failed) attempt to free his fellow Darkspawn from compulsion. After that, he seems to have learned his lesson and is trying to convert the Darkspawn one at a time. (he attempted to convert them in bulk again, with the Mother - but really, can you blame the guy for wanting to get the job done as fast as possible?) And the ritual itself isn't lethal. He kidnaps you and your party during Awakening, drains enough of your blood for the ritual, and you escape otherwise unharmed. He has refined his methods so as to cause the least amount of destruction to the outside world.
Secondly; the Darkspawn he has released from compulsion have demonstrated they can either be good, or they can be bad. (like any other sentient race) However, they are no longer under the compulsion of the Old Gods. Even if some can not handle the "silence", as the Mother puts it, and go mad - they aren't going to seek out an Old God, create an Archdemon, and begin another Blight. Sure, they might lash out and attack the other races in an attempt to commit suicide-by Grey Wardens (like the Mother did) to end their pain. However, as characters like the Messenger proved, those Darkspawn who *don't* go mad, will likely help the Grey Wardens stand against the ones who do.
So at the end of the day, you're cutting the Darkspawn forces in about half, and adding that half to your own forces. And you're taking the Archdemons out of the equation - since if they can't hear the Old Gods calls, it's going to be that much more difficult to find them. Of course, this is only if the Architect succeeds in his plans. Which is going to be a lot harder to do if you're going to try killing him, just because you're prejudiced against all Darkspawn. 