Not quite sure what you mean ...
Anyway, I don't understand why you can't use the "contentfolder" parameter. For example, you have two galleries:
content/public/
content/private/
For the public gallery, make your url:
gallery/?contentfolder=content/public/
For the private gallery, make your url:
gallery/?contentfolder=content/private/
Both those galleries will display a menu created from subfolder of each contentfolder. To make sure the "private" folder doesn't display when someone accesses "gallery/?contentfolder=content/", you can set the "private" folder to hidden, and it won't display in the menu.
Moreover, if you don't want to display url parameters "?contentfolder=content/private/", you can make a copy of the "index.php" source, call it "private.php", and embed the contentfolder directly in the document:
var flashVars = {
contentfolder: 'content/private/', ...