Middle mouse paste is an old common Unix idiom. KDE allows you to turn if off, but this “off feature” is not a standard and KDE can’t prevent non-KDE apps from continuing to interpret middle click as “paste from selection”.
The only thing to do, maybe, is to have some sort of process that tries to destroy other applications support for the “selection clipboard” by monitoring it and as soon as it sees something in the selection clipboard - it takes it over and clears it. I’m not familiar with something that does this, but I can think of a few ways to create such a thing.