Yeah but the mortalitasi had the backing of wealth, names like Pentaghast and a nation powerful enough to rival Orlais.
Rivain is poor, isolated, weak, divided. The Seers never stood a chance.
That shouldn't matter though, the Seekers have their duty and the Chant is clear. Mages like Mortalitiasi shouldn't exist in any position of power outside the Circle let alone be allowed to raise families, right? Or perhaps the Seekers realized the Mortalitiasi weren't actually a threat to the common people and should be allowed to tend their mausoleums.
According to Chantry law, which take precedence over everyone else in matter regarding mages except for the Right of Conscription, Abominations are killed on sight unless there is an option to remove only the demon.
Since the Rivaini mages refused to comply by the rules of the Circle, logic dictates they also refused to have their demons removed. Hence, by Chantry law, the Seekers had every right to kill them.
It's not a matter of official rulings, which is pretty hypocritical and constantly gets twisted or shrugged off whenever a mage happens to be a noble, but whether the Seers were such threat to the people that the rite of annulment was required in a pragmatic sense. The Rivani were from accounts fine with the Seers and even allowed them to lead their communities. Add that to the fact their relationship with the Templars was apparently, and don't see why they would bother using such an extreme measure such as the rite of annulment, when the Seers abominations weren't doing anything immediately dangerous. No demonic abominations running around, no Anders blowing up chantries, nothing worthy of the rite.
Yes, they are savages without any civilization to speak of. Did you miss that?
They have a culture, religion, societal norms and a form of leadership. They aren't savages just because they wear animal hides for warmth and it doesn't marginalize the fact that they have rituals and knowledge that can increase the Circles information about possession and exorcism. Why not use that knowledge for the benefit of everyone?