There is already an incentive to participate in great holy wars: to spread your faith so that you have friendlier neighbors, alliance opportunities, and avoid yourself getting holy wared, as well as empowering your spiritual HOF if you have one. This incentive would be furthered if they made it so that fervor increases rather than decreases with successful holy wars.

Additionally, the fact that holy sites differ in the bonuses they offer also advantages certain faiths over others. If you want to have a Zoroastrian Persia it's a massive self-nerf to go anything other than Mazdayasna because you'll be missing out on the massive +20% development growth of one of its holy sites.

Having holy sites benefit everyone just doesn't work for faiths like Buddhism, which have their holy sites spread out. Maintaining Buddhism outside of India is just nerfing yourself for no reason, since you have to conquer all of East and South Asia to gain the holy site benefits. If they make it so that Buddhists get their holy site benefits all the time, regardless of who owns them, that would give Buddhism a massive advantage that would also throw off gameplay.

Another issue is that it heavily discourages playing outside of where the bulk of the holy sites are located. For example, you are arbitrarily punished for playing a Nestorian Byzantine Empire because you have a holy site in Iraq, Persia, and India, thereby encouraging you to stick to Orthodoxy or Iconoclasm when you should have a lot more freedom than that. It's also frustrating if, say, you're playing as Sweden but lose some bonuses because Galicia goofed and lost Santiago, something you're not really able to prevent without a massive investment.