Why do you have to kill or banish people who you disagree with? I don't understand your line of reasoning at all. At this moment the two of us apparently do not completely agree - must one of us be killed or banished? Obviously not.
We aren't killing each other because we both believe in individualism. "You go your way and I'll go mine". It isn't any of my business what you think as long as it doesn't interfere with me. This is an idea invented rather recently by especially cultivated Brits.
Look at the Uighurs and the Rohingya. That's what happens when a group exists outside some political consensus in the absence of individualism. History is chock full of wars and genocides that are incomprehensible to us because we believe in individualism and those people didn't.
Why would the Catholic Church give a shit about the Cathars? It makes no sense to us, but they did, enough to kill as many Cathars as they could find.