If a whole different stat can be added to describe magic knowledge, that would be perfect. If it´s not possible, then I still think tying the learning stat to magic would be a good idea. The idea of giving mages traits similar to the leadership traits is a good idea as well, and I think both things could work out together.
Let me explain. If a character receives a martial education, he/she can get some leadership traits which are moderated somehow by his/her martial stat. In a similar way, a character who gets a magic education could get some "magic ability" traits (something like that), which describe his preferred magic type. For example, a mage character could get a "Destruction Mage" trait, which would increase both damage made and damage taken for his flank, and these values can be moderated by his learning stat.
Then, if a character gets to have a high learning stat without having a magic education (let´s say, over 20, as suggested earlier), he could get some event where he gets the chance to learn some spells, so he could get a trait similar to those a mentioned above, reflecting the fact that magic can be learned at any time if one has the knowledge. Of course, values should be balanced so that a character who did get a magic education has much greater benefits than a character who delves into magic when already an adult.
This said, I didn´t know extra council spots can be added, so both a court mage and a court priest could be present. That would be cool.