Well if you side with the Templars and Cullen goes off the lyrium many of the Templars follow his example and also go off the lyrium which means while they can use Templar techniques they can't do them as powerfully which makes them less effective for fighting and surpassing mages.
I imagine it also has a impact on the dwarves with less lyrium demand. As for the seekers Cassandra reforming them and rededicating them to their purpose of protecting the innocent likely means its less far likely mages running from the circle will be hunted by seekers unless they start endangering the innocent instead the Seekers will be more hunting down demons and blood mage cults than looking for run away mages.