Communication seems dysfunctional, effort should be made to resolve conflicts verbally with active listening techniques. Avoid escalations like lovers throwing away roommates stuff. This is a red flag for future conflicts, as resentment builds.
Your lover has valid concerns about her safety, and she can take extra precautions. Adding locks or door bars to your bedroom, keeping pepper spray available, and having her communicate and establish boundaries with this roommates lover is good.
Your roommate deserves to have her lover over, you all need to communicate and listen to each other's concerns and feelings.
That was a mammoth read with plenty of "my lover" rather than "my girlfriend/partner" which I found a bit strange. You say "my house" when actually it's not yours, it's a shared, rented apartment and your roomie has as much right as you do with regard to the place.
Anyway, upshot is I think it's actually none of your business if she has anyone to stay over and why should she ask your permission? Why are you judging her partner on the basis that one of your friends assaulted your gf? You obviously knew that person well if they were a 'friend' but they still acted in an inappropriate way so getting to know someone means diddly squat in the grand scheme of things.
As beanspud says, put a lock on your bedroom if it worries you that much but don't try and dictate who does and doesn't stay in a shared apartment.
If you are paying 2/3rds of the rent, or you and your girlfriend are each paying 1/3rd and your other roommate is only paying 1/3rd, then your roommate is not necessarily entitled to have somebody staying overnight.
BUT, if you're paying half, and your roommate is paying half, then your roommate is entitled to have somebody stay over too, as often as you do.
I'm sorry to say, but there's not very much to be done about it.
As others have said, locks on doors, etc. could be helpful if your girlfriend feels insecure about it.
At the most extreme, you can contact the actual owner of the property, and that owner may make a ruling on it prohibiting the boyfriend from staying over (the owner might also decide three people aren't allowed to stay there). Your only recourse against the actual owner or manager is court.