I agree that she would probably have to marry a Protestant prince. However I don't think that it would be a prince like William of Orange, since I don't think that Charles or the Parliament would want that level of continental entanglement. So maybe the second son of a Prussian King or a spare son of one of the Protestant German Electors?
This kind of union could end up playing havoc with English foreign policy, especially if a spare son ends up having to become the (King, Duke, Elector) of his homeland. So under these conditions I would say find the most interesting spare son available on the continent, wait a few years, and then kill off anyone in his line between him and the throne.
Well, if you want something weird, what about this: Charles II has several children with his wife (let's suppose she is
Marguerite Louise of Orleans, as she is Catholic, French and a relative of Louis XIV), but only two survive childhood: the prince James (born in 1667) and princess Margaret (born in 1670). Charles still dies in 1685, and his son becomes James II, who still continues the pro-Catholic policies of his father and now is influenced by his uncle James, Duke of York (IOTL king James II).
However, in order to calm down the most worried Protestants the king decides to choose as husband of his wife a family that is recognized as champions of Protestantism: the Wettin of Sazony. And so, in 1692 Margaret marries Frederick August, the younger brother of John George IV, Elector of Saxony. However, something goes wrong. James II dies (maybe deposed) childless in 1694, and Margaret becomes queen. However, also in 1694 John George died childless, and then Frederick August becomes the elector. Saxony and England/Scotland are going to be in personal union under the House of Wettin.
Ironically enough, IOTL Frederick Augustus would convert to Catholicism in order to become king of Poland in 1697. But ITTL, as he is king consort of England and Scotland he would probably not do it (why the effort of try to be elected king of Poland if you have already secured for your children a more prestigious realm).