SpoilerI think all it did was set the tone for how you dealt with him. You either have an obvious and strong force, weakened by corruption and possible betrayals with a very obvious public face. Or you have a spy army essentially, weak if you were going to out and out fight him. My thinking would be - if you wanted to stop him and not kill him - it would be disband the inquisition and hit him with spies and trading favors.
Though I think they may consider a multi-protagonists
Spoiler
In the long run, it might be best to dismantle the Inquisition, or at least pare it down as in the other choice. Solas claims he has spies in your forces, so many that the Qunari spies stumbled onto them first. When dealing with him, the more chance one has to surprise him might be best...so one wouldn't want to have to worry about this big organization with huge potential for leaks.















