This currently isn't possible - though, as you have mentioned, there are ways to disable the MOUSE 3 button - or remap it- none of those get at the source of the issue. The X11 Primary Selection.
While this isn't a solution, hopefully this explanation will make it clear WHY. In Ubuntu there are two clipboards at work. One, which everyone is familiar with, the freedesktop.org clipboard (captures Ctrl+C command) The second is a clipboard manager that has been at play since before Ubuntu even existed - X11. The X Server (X11) manages three other clipboards: Primary Selection, Secondary Selection, and Clipboard. When you select text with your pointer it gets copied to a buffer in the XServer, the Primary Selection, and awaits pasting by means of the Mouse 3 button. The other two were designed to be used by other applications in a means to share a common clipboard between applications. In this case the freedesktop.org clipboard manager in Ubuntu already does this for us.
Through the extent of my research I can not find a way to disable the X11 selection manager. There are no compilation flags, applications, or configuration values that can disable this. There are various ways around this on a per application basis (majority of these applications being command line ones) - but nothing on a global scale.
I realize this isn't an ideal solution - but seems to be the truth to the issue. The only relevant solution I could muster is actually a hack, create a script that executes an infinite while loop that just replaces the Primary Selection with a null value.
First install xsel (Tool for manipulation of the X selection) sudo apt-get install xsel
The code is as follows:
while(true)
do
echo -n | xsel -n -i
sleep 0.5
done
If you place this in a script and add it to your startup scripts this shouldn't be an issue.