Hi lottrbacchus,
I destroy the other religious building when my faction's religion is different from it, because it provides an awful 15% penalty. It unfortunately adds +5% to religious unrest due to the governor having a different religion and +10% to religious unrest because the faction leader has a different religion. If you destroy it then the city instantly becomes unhappy as the governor's/faction leader's religion, which is different to the whole of the cities population, becomes the official religion. Riots will most certainly start, but it is worth it once you have finished. Once the whole city is converted it makes the city much easier to control - you still get good temple bonuses and you lose 15% unrest at the same time. You also lose all the nasty unrest that was gained from destroying the original temple building and help border provinces convert to your faith too. This can cause large amounts of unrest in bordering enemy provinces and reduction in "heretical" unrest causing faith in yours. I hope this help you. Cheers!