This little script below will overwrite xterm and use mate-terminal instead, for applications ignoring that xterm sucks. It's written for use with monodevelop, but it should work with little to no edit with any other application.
If you have xterm installed beforehand, uninstall it now or a package manager update will overwrite this script. To install it, simply copy the script to
/usr/bin and rename it
chmod +x /usr/bin/xterm and you're done.