In theory an ordeal can cause any flaw. I am wondering how some flaws (specifically pagan) might be acquired... especially for someone self initiating with a script. Part of my thinking here is that its seems an appropriate flaw to pair with Theurgical mysteries...
Pious comes to mind.
As would necessary conditions of casting that would reflect a certain god or daemon that was a central influence on the developing cult.
Also, taking hints from Warping scars, perhaps the magi must either permanently scar their essential form or perhaps their essence nature is changed by some feature of the god or daemon they are involved with. In the same way Mythic blood or Hyperborean blood or Fairy blood changes some physical aspect of a mage, perhaps some minor flaw giving them godlike demeanors.
Possibly ones which cannot be hidden my magic? Though that might be more a Major Flaw.
It depends on why the flaws are being picked. If the flaws result because that's how the ancient texts have it done that's one thing. You get a similar result if its a brilliant, but not overly practical mystagogue who made the script. If they happen because they symbolically represent or align with a goddess, a concept or whatever you'll get something different. If they are specifically chosen for the good of the cult that is different as well.
- So if its an ancient text/unique mystagogue you get whatever they tell you to take. Why? It works, and the authority says so. Its totally fitting for the time. In this case you need to be a pagan for the mystery to work! No one knows why. The ritual may include some mystical rituals to help you get to the right thought process, but it also might include more normal indoctrination procedures. However its unlikely that these rituals are clearly understood to be indoctrination procedures.
- If its because it aligns with some concept core to the cult. For the case of pagan its because the cult is dedicated to a pagan concept, or perhaps some great hero central to the cult was a pagan. This is similar to the first except there is a very clear idea of why this is the case. The rituals may include indoctrination, but again it might not be understood the purpose of the rituals.
- Cult leaders chose pagan for their own benefit. Only makes sense with more cults that actually understand initiations on a "meta-cult" level. They know that the initiations alter people on a fundamental level and that the initiations can be crafted to make people more useful to them. The main difference here is the only reason for the initiation is because the leaders are trying to distort the cult. There will likely be mystical rituals to enforce it.
If you want to know how to inflict the pagan flaw? Look up how brainwashing, cults, and preachers work. Then note that their is mind control in Mythic Europe.
For theurgy I would say that it involves Pagan worship of Daemons. Between the teaching about Daemons, the magic which they certainly include and the rituals they get dragged too, they end up as a Pagan worshiper by the end of it.
Remember that the pagan flaw mentions the possibility that their gods might punish them for engaging in christian rituals.
In that sense it's easy to grant the flaw: The recipient has to make promises to those gods. If they break those promises they A) lose the virtue gained and B) are Plagued by a Supernatural Entity.
So perhaps a quest to find the forbidden texts, followed by a season studying the texts while living only on a certain tea... giving the flaw pagan and adding +12 to the script, with room for a remote location or other quests if necessary...