Inquisator ruined my crusade!

[Morindin]

In 'theory' inquistors had the power to burn anyone they wished. They generally acted independant of the papacy (although later on the papacy 'recommended' inquisitors).
They had ultimate say over who they went after, regardless of status.

Now that is in theory. In reality they never really went above minor nobles. They mostly targetted people who preached heresy.

There were political motivations for Inquisitions, the most famous of course being the Knights Templar. The French King was the main force behind it, due to his large debt to the Knights Templar, and managed to EVENTUALLY convince the Pope that the Knights performed homosexuality in their secret rituals (which was of course, untrue). He confiscated their lands and treasures. The English King on the other hand let most of the Templars there leave to Ireland and didn't confiscate their lands in the name of the crown.
Joan of Arc was another famous victim of political inquisition, due to the fact she wore mens clothing (which were more comfortable to fight in). The full force of the English crown was behind her burning.

So all in all Inquisitors 'in theory' could go after whom ever they pleased, but they rarely did. They mostly went after heretical preachers.
If it was a matter of historical accuracy, I think they should be limited to Witches, Heretics, and low piety Priests. They should not really go after Kings, Royal Families, Merchants, or Generals.
Perhaps inquisitors in your lands could cause extra unrest due if you are acting like a heretic it would look bad on your people, but they should leave your main family members alone.