Your roommate will feel like he/she is intruding no matter how often you say, "No! It's fine!" Your roommate will only feel comfortable in his/her room and will resent you for it. Not to say that you are responsible for the feelings of your roommate, but I'm just letting you know.
Worst off, your roommate will feel like he/she is living in the kitchen of the McDonald's of your relationship. He/She will see and hear things that make him/her sick, and can't do anything about it. He/She will notice how your girl/boyfriend is a complete baby who can barely do anything without you. Your roommate will get first hand experience with how grumpy your girl/boyfriend is in the morning. Your roommate isn't sleeping with your houseguest...he/she shouldn't have to deal with a pissy person that's not you.
So, next time you present the idea to your roommate that you want someone to stay with you for a long time, be aware that he/she will say, "Of course, it's fine!" But your roommate will really mean, "Oh God, no!"
If you cannot do anything about the extended visit, make it clear to your guest that he/she must try to get the hell out of the house every once in a while. That your roommate doesn't want to see your guest's face EVERY time your roommate comes home, no matter what time of the day or night.
Feel free to ignore this advice...but at your own peril.