How about I tell my roommate his friend can't stay in his room when no one else is in the house.
Sounds reasonable. What is that friend is always there no matter what?
I don't want to inform him, I'm just going to take action immediately
This is not only your place, but your roommate's place too. Your roommate is still respecting all the boundaries by just having the friend stay in his room. You have no right to tell him to leave, this isn't your house only.
No I am planning to piss off my roommate and ruin his friendships.
The only thing you are ruining is your living situation. He might get you kicked out for interfering with his personal life. You both pay rent so you don't get to dictate what he does.