the program should can be disabled for each user with a simple ckeckbox, what means disabling every feature for that user. if it is possible, stopping the service after disabling the program would be great.
You want to disable Classic Start Menu per-user on Windows 8? Then disable the service, and for whatever users you want to start it, add a shortcut to C:\Program Files\Classic Shell\ClassicStartMenu.exe to that user's Startup folder in %appdata%\Microsoft\Windows\Start Menu\Programs\Startup. That will make it start only for specific users. Note that disabling the service also disables the ability to skip the Start screen for every user.
This is explained in the FAQ: http://classicshell.sourceforge.net/faq.html#menu_user
Another way is to let it run for all users, but for some users disable the start button and change the controls to always go to the start screen.