You can use: gsettings set org.mate.Marco.global-keybindings switch-to-workspace-left disabled gsettings set org.mate.Marco.global-keybindings switch-to-workspace-right disabled gsettings set org.mate.Marco.global-keybindings switch-to-workspace-up disabled gsettings set org.mate.Marco.global-keybindings switch-to-workspace-down disabled
The names of those (and many other) settings can be found here (in somewhat unreadable form): https://github.com/mate-desktop/marco/blob/master/src/org.mate.marco.gschema.xml. The command for changing shortcuts is described very shortly in https://github.com/mate-desktop/marco/blob/master/README.