Talk to your roommate, you have to let him know that she is starting to cause issues and see if you can come an agreement on visitors. On the other hand, be happy it's just some awkwardness and space issues, it could be WAY worse; I had a situation like yours, only the girl wasn't hot and SWAT was almost called to our house.
I was living in a house with two other dudes, one owned the house, and the other was renting like me. The guy who was renting got fired from his job a week after moving in (I had moved in the week after him) so he just sat around the house all day with his CRAZY GF (who pretty much lived there) and they ate our food, left every damn light on, had hour long sex showers and were overall a drain (If I can find pics of the utility bills I'll post them, it was insane.).
It got to the point where the owner was trying to kick them out, because of the above issues and only paid enough to keep him from evicting them. Then they both disappeared with no warning, but every now and then we saw signs of someone at the house when we were gone. I then found a note on our front door from a friend of the roommate letting us know he was in jail, so I looked up the police blotter for my town and found that our roommate and his GF got into an epic fight; here are the bullet points:
• RM tried to kick GF out
• She locked herself in the bathroom
• RM went and got his AR-15 and told her he was going to shoot the door down
• GF called police
• 5 squad cars showed up to the house
• RM went to jail
So I saw this and understood why suddenly no one on our street would talk to us, then called the owner and gave him the lowdown. Later that week the owner and I got home one day and saw a land phone had been installed on the wall, he asked me about it because he was pissed I did it without asking. I told him I thought HE had it installed and it was about that time we both realized why stuff seemed to be moving around while we were gone; the crazy GF had a key to the house from her jailed BF and was moving her stuff in while the two of us were gone at work!
The owner started the eviction paperwork and after a few more arguments and another visit from the police we got them out and changed the locks.
Good fun all around.