You question is intriguing, and I am uncertain. The direction of my clan's leadership would have been very important. To fight for James (Jacobus) even though they of late were faulty and misdirected kings or to fight for bloody England and parlament... It kind of reminds me of a typical American election for President or Congress: the choice of one lying incompetant moron or a lying crooked shyster. I would have probably fought to defend the honor and dignity of the office of the rightful king (alias the Pretender's son), not for the person(s) and their behavior involved, and thus a vote for the good of my nation's civilization. Which ironically would have made me a bloody rebel.
Yet if my sept or clan lived in the lowlands, the risk would have been great indeed to side either way, since it was a blended English-Scottish no-mans land with blended loyalties. If I had lived in England along the trek which Prince Charlie invaded England to reclaim the throne, I just might have joined him (yea, at the most fateful hour).
However, I most certainly would have been with the noble James Graham, the 1st Marquees of Montrose, before that in 1638 at Grey Friars Churchyard to sign the National Covenant and so fight against the religious tyranny of forcing all Scots (against personal conviction and conscience) to worship according Laud's Book of Common Prayer, or else. I say this even though I am a Lutheran Christian, one who honors in faith and practice the Biblical Word of only non-sodomizing men as elligible for the office of the holy ministry. But I digress...
Conclusion of the National Covenant:
"From the knowledge and conscience of our duty to God, to our king and country, without any worldly respect or inducement, we promise and swear by the great name of the LORD our God to continue in the profession and obedience of the aforesaid religion; that we shall defend the same, and resist all these contrary errors and corruptions according to our vocation, and the the utmost of that power that God hath put into our hands, all the days of our life."