I don't really have anything to add or change with the disaster, my issue is its rarity as you mentioned. Changing the requirement for 75% or less religious unity to 90% or less would probably be too extreme.They do theoratically have their own disaster (https://eu4.paradoxwikis.com/French_Wars_of_Religion), but it barely ever fires. What would you do to represent it though? Here's a event, if gives you a stab hit and now everyone's a heretic cos screw you for playing France? The root issue, IMO, is the inability to represent religious minorities/oppression terribly well in EU-the same reason the Lollards are represented in England with a 'here's a doomstack, go kill it' mechanic. Short of making immensely complicated, bloated modifiers everywhere (hello, MEIOU and Taxes), you've either got to punish certain countries for choices they may not even have made in the game's timeline cos history, or accept that some issues have to be simplified to make a playable game.
Ideally, changing the way that CoRs spread their faith will make this disaster more likely. Stop focusing Italy, particularly the Pope (who can't convert), and start focusing France and Sweden (who hardly ever converts because even a CoR in Denmark isn't enough to convert enough of Sweden's provinces). This is really the root of my grievance.