I noticed while installing plus through an older installer and deselecting the example levels, that once I updated the game through the updater, the levels were added back in. Maybe it could be an option to use the users settings they used while first installing plus for further updates?

Some ideas as to how this could be done: either by looking in the JJ2 installation folder, and if none of the plus example levels are there, don't add them. Another option, which might be neater, is to add a section to plus.ini with the installation settings and read that when the updater is doing its thing?