Revya wrote...
I was able to persuade the peasents to leave with little fuss, but when the ending stated that I gave them what they wanted. I did a double take...when did I ever give them anything I just said "trust me"...politicians say the same thing all the time and I don't see them granting wishs. So I have to assume that its a bug if not than its lack of forsight.
I also was able to persuade the peasants and they just gave up and went home. It was the easiest resolution to any of the ruling problems I encountered.

There wasn't any mention of it in the epilogue at all that I recall for my ending.
The choice between Amaranthine and Vigil's Keep, however, was the most devastating for me. It really bummed me out to lose the Vigil and the lives of three of my companions. My character was left wondering if he had just paid the dwarf the extra gold he wanted for skilled laborers- would that have made a difference? Would the Vigil have held? But those runes were so damn expensive! Aaarrghh!

My character wanted his Wardens to have the best equipment gold could buy, but great equipment doesn't do you any good if you're overrun by a horde of darkspawn because your commander was too cheap to make sure the walls were as stout as possible. Oh, the guilt. I imagine it's why he resigned his command and wandered off after Morrigan. Maybe, like Ohgren, he's "only good at killing things", not ruling over people.
If you ally with the Architect at the end, it does say the Deep Roads grow quieter over the next several years than anyone can remember. Surely that is due to the influence of the Architect enlightening his brethren? Even if he dies, doubtless he has disciples who will carry on his work, even if his genius would be missed. His disciples don't seem to possess his restainst and self-control, however.
Once the seventh is dead, you're free to head into the deep roads and systematically slaughter them. There's no driving force calling them, and they are unintelligent, so they won't organize. They can be hunted down.
But they are still tainted. That would be the major problem, I think. Most people die when exposed to the taint, sooner or later- mostly sooner. Trying to chase them down into their corruption-filled holes deep, deep underground would result in unsustainable casualties to the soldiers from the taint and disease, I'm thinking. I'm not sure losing their compulsions would make them any less organized. They're pretty unorganized as it is. But they would still have their hive mind. What one knows, all know. I don't think it would be possible to eradicate them. If anything, your best shot would be when they're gathered in one place, digging toward an Old God. But I think the dwarves would have attempted that a long time ago if it were possible. The taint is just too much to overcome.