I think anything can happen. From what I have seen at work, the Scots could be pretty pragmatic and skeptical when needed, but they are also very empty-headed and emotional when it comes to talks about nationhood and symbolism. I believe they are capable of being that reckless to go for the Jacobite monarch if Scotland does become independent.
Of course, we in the Commonwealth needs to prepare for the worst. “Who will be our head of state” may not be a mere academic exercise.
The Scots will either keep the monarchy or become a republic. The Jacobite “option” isn’t even on the table. It is a dead issue for all except a few eccentric cranks. We aren’t living in the early 18th century anymore. Besides which, Jacobism isn’t the same as Scottish Nationalism, the Jacobite line heir to the thrones of England and Ireland (well, the Northern Part) as well...