Thanks Yoshi but I found another legit way... thought I expect it to be a bug of omission... If you allow yourself to be force converted (By negotiating with religious rebels) you will lose the Religious_Turmoil modifier. So in my case, I get Ecumenism then I negotiate to convert to Protestant (Or reformed) then I lose the Religious Turmoil and never get it back since Ecumenism prevent it to activate. So now I get to have a Innovative tolerant state without constant rebellion. (I have +3 Tolerance of Heretics and +4 Tolerance of Protestant).
I believe that the intent of Paradox in this case was to have Ecumenism remove the Religious_Turmoil but they forgot to do it or something. Also if you look in the History files, the Edict of Nantes is supposed to remove the Religious Turmoil too but there's no event for it.
As proof from French History File:
1598.4.13 = { clr_country_flag = religious_turmoil clr_country_flag = religious_intolerance decision = enact_edict_de_nantes } # Edict of Nantes
Anyway in short, if you get hit by religious turmoil and want to be a tolerant (if not secular) state, get ecumenism then force convert by negotiating with religious rebels and religious turmoil will be removed and you'll never get it back.