If you can take the province, you can usually convert it. I destroyed a couple centers that way in the Mulhouse run I did.
Center of reformation is -5%, you get a base of 2%, 2% from inquisitor, and 1% from state edict by default. To get positive conversion strength, you then only need enough strength from decisions and ideas to overcome the modifier from development.
Since you can get another 1% from estate and will almost certainly have multiple decisions giving some strength, it is very likely that you will convert it faster using a missionary than you can convert it by making it the last province of target and then executing a follow-up war, even without religious ideas.