Even the Templars in Tevinter are not proper Templars, so may be the Magisters have just got complacent since the break with the southern Chantry. The Seekers were formed in the south specifically to deal with demons and malifacarum and were pretty secretive about the source of their abilities since even though own members are unaware of how they come by them, so I imagine the Lord Seeker would be very careful not to let anyone outside the Order learn of exactly what they can do and since the main ability to resist possession is acquired by essentially becoming tranquil, it is not something the majority of mages would be keen to dabble in.
Actually, thinking about it, the Magisters must have done some research or acquired some degree of information because they do know about the Rite of Tranquility - they use it to punish dissidents. However, they don't know about being able to reverse it (or not publically anyway) since Dorian asks Cassandra if the rumours are true, since he knows people who have been punished with tranquillity in Tevinter and I dare say would like to be able to help them.