Well since I'd only heard WoG on the comics pretty recently, I've always assumed that Alistair was right in Origins. Templars develop their powers without lyrium through training, then are given lyrium only after taking Templar vows. That the lyrium amplifies their skills. Lyrium addiction is not a secret. What is annoying me is that the Seekers for some reason or another have hidden something that means the addiction wouldn't happen...that is...well I'm too polite to say what I shouted at the screen earlier today. 
An army deliberately addicted to lyrium that is distributed officially by the Chantry...places a lot of power in the hands of the Divine. 
Did the Seekers keep the secret from the Divine as well? Thus maintaining their independence from control, or are they fully culpable of collusion?
My Warden, Hawke and Trevelyan would all like to know...Cassandra I'm going to make your interrogation of Varric look like a park walk....SIT! If she argues, I'm telling Cullen and his Templar...I don't think they'd be amused either.
On the plus side we now have a possible way of bringing renegade Templar back into the fold, if it is even possible to apply this addiction cure to those already addicted.
I see the Chantry being reformed at the point of Templar swords.