I’ll admit I have not read Popper. But just because he coined the term doesn’t mean his conception of it is the only acceptable one. Others have taken the basic idea and taken it in different directions.
Specifically, if someone is intolerant of others in a way that rejects who they are (as opposed to rejecting something that they believe—so gender and sexuality are on one side of that line, while religion and political ideology are on the other), especially if they do so in a way that creates the feeling of an unsafe environment, we should feel perfectly fine excluding them from that space.