One workaround could be to clear the selection clipboard manually using a program like xclip. Then even though middle click still pastes the selection, nothing happens because the selection is empty. That is:
This clears the selection once in 10 seconds.
while true; do
xclip -i /dev/null
The downside is that many X programs seem function so that once the selection is cleared, then also the highlighted text is cleared in the program.
For example: In Lyx, when one highlights a part of a text, this is copied by the X server. When the script above clears the selection, then the highlighted text in Lyx is no longer highlighted.