Should I feel bad that I walked into my flatmate's room while she was having sex and refused to leave
That was rather rude of you. What led you to do that?
I want her to move out of my flat so I'm trying to be a lousy roommate.
Well you shouldn't do that. Just wait until her lease is up and refuse to renew it. Or if you don't own the place you could move yourself.
I wanted to break up in a special way.
Creeping her out isn't a good way to part ways. If you're not comfortable with the living situation you need to talk to her about things you can both improve on. If you really want to end it you could see about getting out of the lease early.