If you're a convert from a pagan religion, shouldn't your chance of being made a saint increase, not decrease? Constantine the Great, Miran III of Iberia (Georgia), Olaf II of Norway, Vladimir the Great of the Kievan Rus', and Stephen I of Hungary are all venerated as saints pretty much solely because they converted (Constantine didn't even really convert until his deathbed). I'm not sure if there's a way to check if the person is the first Christian ruler of a Kingdom title, or whether most of the de jure kingdom was pagan at the time of their conversion (I suspect not), but if you could it seems like that should provide a small bump to the likelihood of saintliness.
It also seems like those missionary priests who try to convince pagan rulers to convert should get a big boost to their chances. A lot of Saints are either people who converted countries or important people (Saint Patrick is an example of the former, and while Clovis I of France isn't a saint, his wife Clotilde, who convinced him to convert, is an example of the latter) or people who were martyred for trying to convert people (Saint Alban, for instance).
By the by, the Eastern Orthodox Church also makes people saints. Of course, there it's "Glorification" instead of "Canonization" and is a different process. Plus, Orthodox Saints who were responsible for spreading Christianity by leaps and bounds get the "Equal-to-the-Apostles" title, which is badass.
Just a thought, if you don't already have enough ideas for expanding the mod, haha.