In general,
I really like the mechanism as it mirrors likely civil unrest after a foreign religious takeover. Plus, it allows a greater cultural diversity since converting rulers may stay in power. I really like that.
Yet, I have to assent to the OP's argument, that the rebels forces tend to be too strong. So maybe consider toning their strength down, a little dear dev's? Or, even better, create a game rule which allows three to four intervals (weak (0.5), normal (1.0), strong (2), very strong (3)) to suit the individual player's preference in terms of challenge.
And on top of that, please consider extending such a religious rebellion mechanism to a greater variety of CB (e.g. Muslim invasion, as mentioned above) so that people not simply discard of the duchy holy war-CB as to risky in the long run![]()
Because the Crusaders totally faced massive peasant doomstacks after conquering the Levant...
And the Iberians faced massive revolts after taking over Andalusia...
I think that HIP, like Meiou and Taxes, tends to take a nerfbat to doing "ahistorical" conquests (specifically, in this case, things involving wrong religion and such), ignoring that 1) this is supposed to be a sandbox game, and 2) that's not how history worked. Granted Paradox doesn't allow for much nuance (at the very least, religion/culture should be proportional rather than a binary factor), but even so, it doesn't make for fun or engaging gameplay IMHO.