I agree that it’s unreasonable for the BF to sleep in the same room as you.
I assume they did it because the futon is uncomfortable. Between their own discomfort – and your (reasonable) discomfort with the alternative, which is sleeping in your room – they made the only rational decision. Wanting to sleep together, they will get their own place.
Sadly, this is what happens when people grow, meet significant others, and want to spend time with them. Definitely hold your roommate to whatever she signed: she shouldn’t leave you high and dry with the rent.
But in the end, there’s not much you can do about the situation. It’s hard to lose a roommate. It’s doubly hard when the roommate is also your best friend. If this friendship is important to you, let them go graciously. Odds are their romance won’t last (most college relationships don’t) but even if it does, a true friendship is worth a bump here and there.