I have already used the "mu-plugins" directory technique. Even with that I somehow did not manage to have the desired result. i don't think it can be achieved and as andrea_r pointed
It will run all the time, and it will not hide menu items from that folder.
Frankly, I find it quite pointless to have someone as an administrator, showing him/her the options to "the plugin" and asking them not to touch it. Furthermore, some people do not take it lightly if they are told not to mess around with the settings. In some cases I even had reactions like: "Why, do you think I'm dumb?", "I'm the admin, I can do whatever I want", "I am the client. It is my database. If I make a mistake it is my own responsibility", "You worry too much. Relax".
On the other hand, I do not think it is an issue that should be addressed by individual plugin developers. At this very moment the plugins counter reads 10160.
When we run a multi site we cannot expect a uniform knowledge and behaviour by all administrators. What happens now is: You don't get to show the plugins activated on their site, but they still see and can mess around with their options. They can even see the little cloud saying "Six to be updated".
Furthermore, there are plugins that should be touched by experienced admins ONLY.
So, I definitely believe that it has to be addressed -as I mentioned before- in a much deeper level while still in the core of the system.
Till then the right plugin will do. Any suggestions?