First you need at least one (preferably more) hardcore gay porno mags, and a frying pan. Then when the roommate is out, you and your man retire to the bedroom. Put the magazines ON your roommate's bed, the frying pan under your own pillow, then you and your man cuddle up and go to sleep.
When the roommate comes home and walks in and sees you two, if he's cool he'll let you sleep and not make a big deal of it (problem solved). If he *isn't* cool, he'll either leave without waking you and come back a while later with a moving truck for his stuff (problem solved) OR you'll wake up to him freaking out, at which point you point accusingly at the magazines on his bed and say "well when I saw THOSE I assumed we wouldn't have a problem, ya big homo!" He'll be so surprised, confused and horrified by this that he'll be disarmed for a moment, at a loss for words.
That's when you hit him in the face with the frying pan, as hard as you can. Then you hit him again. And then again. And after the twitching stops, you and your bf bury the body somewhere. (problem solved)