I believe Logan was an accident. Sid is part of Em's life. He can't be removed.
The only thing that could be done is to adapt to the situation. Because Sid is just a guest, he can be asked to go for a couple of days. And Lisa has the power to do that if she wants to invite guys like before.
It's obvious that Em will no longer have casual sex in this apt unless Sid is ok with that, but that will not happen.
The other solution to raise the level of this apt with Sid and Em would be to bring regularly back the girl with whom they had a threesome. Sid like it, Em like it. They will all be happy and the viewers will appreciate that.