I'm imagining something similar (but not identical) as Charlamagne in CK2. For example, let's say Norse paganism is reformed, if you crusade into Norse pagan lands, and manage to get control of all the holy-sites, you should be able to perform something similar to the destruction of Irminsul. I don't think that should turn it into a completely dead faith, but if you control holy-sites, destroy the main worshipping symbols and areas, capture the head of faith, that should make it very difficult for a norse pagan to reform it again.
Maybe the answer is instead of killing it, having an ability to "unreform" a faith?
Not impossible, and I think it could make it an interesting challenge to attempt to revive these faith's.
Although, I think this should be something with incredible consequences. Maybe as a ruler, you have a choice to persecute the Samaritan priesthood if they reside within your area, or attempt to foster religious tolerance which might lead to positive development etc, but the attempt of destroying a minority religion like that should be controversial, and filled with potential consequences. There is a reason why the consequences of those rulers choosing to persecute smaller religions or choosing to be tolerant still exist today.