I just finished Awakening yesterday and my Warden spared him. I have been agonizing over whether that decision was in-character since.
Here's how I looked at it at that moment -
Does the Architect deserve to die: The Architect is responsible for the attack on Vigil's Keep. It may have been a misunderstanding, but people died. The Architect, through his agent the Seeker, is also responsible for the death of the Dalish Elves in the Wending Wood and partially responsible for Velanna going crazy and murdering all those merchants.
My Warden chose to execute Loghain for his crimes. The Architect fits the bill for that sort of justice as well, from her estimation.
However, if the Architect is right and this reverse Joining can free darkspawn from the control of the Old Gods/Archdemons, what are the possibilities?
Best-case Scenario: The freed darkspawn have run the gamut from insane (The Mother) to devious (The Lost) to loyal and helpful (The Messenger). From this reduced sample, we can imagine that a race of darkspawn would be just as diverse in their outlook and mentality as any other race. If the darkspawn are truly freed from the urge to seek out and awaken the Old Gods, the Blights can be pushed back centuries or even postponed indefinitely. Most importantly, the darkspawn assault on Orzammar might weaken or even cease. The example of Armaas, the Tal-vashoth merchant, shows that these intelligent darkspawn can even honour trade agreements. The taint is still an issue, but any disease can be cured or contained.
Worst-case Scenario: The Blights are dangerous, because Archdemons are fiendishly intelligent and compel the darkspawn to attack the surface lands, making them an organized army instead of a horde of mindless monsters. What do we see when a Blight ends and intelligent darkspawn are running around on their own? Organized armies attacking the surface lands. Intelligent darkspawn potentially means unending Blights, where darkspawn forces are capable of coordinated assault in the absence of an Archdemon leading them. This is an incredible threat. Intelligent darkspawn can also mean more concentrated efforts to find and release the Old Gods, meaning instead of centuries between Blights, it can be decades.
To sum up, best-case scenario - Darkspawn cease their assaults and you can treat with them as much as you can treat with any other race. Wonderful.
Worst-case scenario - Darkspawn never cease their assaults and continue to plague the lands, even after a true Blight has ended. Horrible.
On the face of it, being a Grey Warden, you should err for the status quo and kill the Architect. The chances of things going bad are high (especially when you later learn the Architect in his naivete was responsible for awakening Urthemiel and starting the Fifth Blight). I play my City Elf Warden as compassionate and empathetic, but also pragmatic. She destroyed the Anvil of the Void and refused to leave Amaranthine to it's fate for example, but she also betrayed Harrowmont and chose Bhelen for the throne and convinced Alistair to do the Dark Ritual, knowing the risks of letting Morrigan bring some Old God/human abomination into the world. She does the right thing, but she is fully willing to do heinous things to succeed if necessary.
Like someone further up the thread, I also hoped that there would be the opportunity to engage the Architect after the fight with the Mother was over, but that was not to be. So, my Warden spared the Architect, going through the following thought process -
The Mother and the Architect are enemies and the Architect is a potential ally against the Mother. The Mother is aggressively hostile to everyone; the Architect's motives are far more ambiguous. He can help. I can deal with him later.
If the Architect is right - and there is a former Grey Warden following him...maybe that's a stamp of approval of sorts - and these darkspawn stop trying to cause another Blight or attack Orzammar...that's great
But then the first thing they did after becoming intelligent was have a civil war and raid surface lands. So...
A series of mini-Blights can be a horrible thing. But I have seen the darkspawn can be helpful and averse to violence...if this idiot learns from his mistakes...the assaults on Orzammar may be weakened and the next Blight may be pushed back a long time, if there are darkspawn actively working to prevent it...if nothing else, with the Mother dead, the Architect will lead the darkspawn and I believe him when he says he does not want a Blight...
'Very well. You have an ally."
Of course, then you find out the Architect caused a Blight in trying to avoid a Blight, so...At least the Epilogue shows it paid off in the short term, with darkspawn forces retreating underground and not coming up for at least a decade after Awakening.