I think the easiest way would be to put the files into a password-protected .zip file, since there is no way that I know of to have LabVIEW create a password-protected installer.
Another option is to program your VI such that when you run the executable it asks you for a password, but that, of course, protects from executing the program, not installing it...
You could look into using the unique Product Code that the installer assigns to your program, but I am not sure how the installer interacts with the OS to be able to use this code.
