I think Heresy and Judaism as well as the amounts of religion that each province starts with a are somehow hardcoded. There are events that increase heresy such as the Albigensian Heresy and the Bogomils and Cathars, and I think you can add a "HERETIC(2)" to column 67 to cause an agent or unit to increase heresies, but I'm not at all certain about this. The only way to do what you want, if it is even possible, would be to add it to a unit. It doesn't work for buildings as they only propagate the faith of the owning faction. If it does work it could be added to spies and assassins to represent the negative effects on religion, their presence in a province may have. I seems like a very interesting idea.
Edit: It does work for agents, I have added it to spies and assassins which will give a penalty to excessive spy use by the player.
Using this you could create rebel only Jewish Rabbis, Pagan Priests or Heretical "Whatsits". They could be set as hidden, to get them "cleaned off" by your spies and assassins.
Edit2: I was testing it yesterday and it does allow the abuse of spies as "heretic priests" but this also occurs in your own provinces where spies are stationed as counterspies or to improve loyalty. This has to be countered with your own religious agent. To be honest I can't see it working. I've added a 1% modifier to assassins and a 2% to spies. My aim was to add a side effect to storming spies into a rival province as well as trying to convert it to your religion through use of your own priests. Having spies and assassins in your provinces counterspying, would have the side effect of an increase in heresy.
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