Manual:$wgSkipSkins/en

Details
Specify the names of skins that should not be presented in the list of available skins. Use for preventing users from choosing one or more skins which you do not want to remove from the  directory.

Example, in LocalSettings.php put:

Above would remove all skin choices but Vector. Omit from above array any choices that you want to remain.

Changing user preferences when removing a skin
In versions up to 1.16 (at most), upon registration the name of the default skin as provided by  is copied to the user preferences of the user. When you later make this skin inaccessible, use the maintenance script to make sure that this skin is also no longer chosen by any user:

This will change the skin for all registered users, who have selected Monobook, to Vector.