"Limited somewhat" is a rather modest proposal, I think. It is a powerful CB, especially against reformed religions as balmung60 points out. It's especially annoying to watch Asturias being crushed time and again by al-Ándalus, as well as seeing the Miaphysite Ethiopians being gobbled up my Egypt (regardless of start date).
With the introduction of prosperity in Reapers Due, I'd suggest a Tolerance law:
- At minimum Tolerance, you'd be more likely to suffer religious uprisings but the Holy War is fully allowed. Children will also be far more likely to pick up the Zealot trait. You can no longer find pagan/heretic/infidel court physicians. Maybe bonus to piety per month.
- At medium Tolerance, religious uprisings might be slightly less likely but the Holy War is limited somehow. I'm not sure how, but it could possibly be that the target is subjugated rather than lose all titles (similar to de jure CB). If you have religious revocation you can take it anyway so that law could be dependent on Tolerance too.
- At high Tolerance, religious uprisings will be unlikely but you will lose Holy War CB. You will also be more likely to invite infidel courtiers and might receive more Jewish councilors by event (as well as Mu'tazilas if Christian or maybe cynical monks if Muslim). Children will be far more likely to pick up Cynical trait. Unrestricted court physicians and medical treatment. A few prosperity events for infidel provinces. Maybe penalty to piety per month.
This is the general idea, anyhow there should probably be more than three steps. Not too polished either and quite possibly unbalanced.
Anyway, if al-Ándalus starts at high Tolerance they won't be able to invade Asturias, but Asturias can bide their time, ally Frankish realms, and assault revolting vassals. Now, I
know that Muslim tolerance wasn't the historical reason for Asturias' survival, as several posters have pointed out (in other threads) it just wasn't worth conquering. La Convivencia itself is a contentious matter. However, in gameplay terms (and we're talking about a game with one somewhat questionable and one
very questionable start date) it works. And that is more important, I believe.