[@Lexicon]
There's nothing flagrantly against the RP in your idea. I quite like it!

The one issue with runic magic is that it's not necessarily hereditary, much less like witchcraft. That's not to say witchcraft doesn't exist--there are many many ways it can, but runic magic is one of the few scientific approaches that any intellectual can learn. It goes hand in hand with engineering and science of the era (although it could definitely be used to mess with someone's mind, yes.).

So, as your idea is, it's actually fine--you'd just have to cut out the bit about the runic magic being witchcraft.

If you want to keep that more taboo-y mystic-y witchcraftery, I'd suggest making the mother a ghoul, a fae-touched human, or a pagan witch. A ghoul would be the most sinister of these options (meaning the mother is attached to a vampire who may or may not be sanctioned by the baron) and allow for mind control through hypnosis. A fae-touched human could have made some sort of shadowy pact with a fae entity to gain the power to manipulate a mind through phrases, music, dreams, etc. And a pagan witch might have her own cult that worships some unholy entity of Darkness, which allows for some awful sort of life draining or soul manipulation. It's really just picking the flavor of your character's crisis--any of these situations would summon the wrath of the Holy Knights. It would also influence inherited ability, as I'm willing to allow some manner of taint from mother to child (just be aware that such hereditary powers would have their own pact limitations).

One final word of caution is what I've formerly mentioned--if your character is losing both parents, make sure she still has a relevant, healthy and available connection with some friend, family member, or rival that I can use to keep things relevant to the plot. Does she have a family member taking over the estate in her absence? If not, is it a benevolent or greedy entity stepping in to claim her birthright and, consequently, her village? (these are questions to consider in your CS.)