I found it! \o/
To disable alt + right-click when using blender (or any other software where the system binding collides with existing bindings) and re-enabling it when blender quits, i use this in a bash script
gsettings set org.mate.Marco.general mouse-button-modifier ''
/path/to/blender-2.x
gsettings set org.mate.Marco.general mouse-button-modifier '<Alt>'
Make sure it has last empty line and that it's executable and now edit the entry in the main-menu to point to that bash script instead of blender. If you added a shebang on the first line of the bash script such as: #!/usr/bin/env bash
it will work in type "Application" otherwise It needs to be of type "Applicaiton in Terminal" or it wont start.
(And if you use blender bundle from blender.org, don't forget to update the path for blender in the bashscript whenever you download the latest version)