Well, they can't do that if they have a lease agreement together, which is typically required if both are living in the same place. She could insist that he move out because no one can legally force her to leave if she pays her bills... but that might be the key. Stop paying her half of the rent. If she doesn't want to live by your rules, then she needs to start providing for herself. Of course, that's a situation no one wants to live in, so it may just be that he would have to leave in that situation.
However, despite all the comments back and forth, there is one philosophical truth: Based on the information you've provided for us, she doesn't have any desire to live under your authority, and if that's the case, your marriage would end in divorce eventually. However, she wants a standard license so that when she divorces you (or in her mind, if you divorce her), she can take a bunch of property and money with her; without it, she knows she won't have that. That means, whatever you're hoping for currently doesn't exist; therefore, steps should be taken to reflect reality, even though you may not like that reality.