Currently there are blank key bindings availible in FTPSync, so it does not collide with other plugins or your settings or your Operating System. To open the file go to:
Main menu > Preferences > Package Settings > FTPSync > Key Bindings
In the Default file there are templates for setting your key bindings, command names. For more information about key binding in Sublime Text 2 see official documentation (not really in-depth though) and you can see the list of commands.
For the idea thanks to Benjamin Kaiser.