I think you've gotten to the heart of a problem here. I don't think Popper ever intended the paradox of tolerance to apply to speech. I think he was just saying that your right to swing your fist ends where my nose begins. There are a lots of actions, including most speech acts which should be tolerated because they don't hurt anybody (AKA victimless "crimes"). I think that's all he was saying. Certain kinds of lies should not be tolerated if they lead to damaging people other than oneself. Otherwise, Let Freedom Ring.

I think the rise of fascism made people less tolerant of intolerant speech when they saw how much damage it caused. We are in the middle of another Fascist wave, which makes tolerating intolerance seem dangerous again. But not tolerating speech we disagree with is even more dangerous, I think. It's a tricky balance.