Something approximately like this command should do it:
Code:
sudo chflags -R schg /Path/To/TheApp.app
I strongly urge the reading of man-pages for the sudo command, the chflags command, and the chflags(2) system-call. In particular, it will require booting into single-user mode to remove the effects of the schg flag. This is not a trivial undertaking, and may be more onerous to deal with than some other strategies.
As a point of reference, the uchg flag is used for the user-lockable Locked checkbox in the Finder's Get Info window for a file or directory. If you know what dealing with that is like, then imaging that but being irreversible without a reboot and multiple command-line invocations, each of which must be exactly right.
I have used the schg flag on a few occasions, and it is not to be used without due consideration of all the consequences. It's one of those "be careful what you wish for" kinds of things.
Also, I have not tested the above command-line, which is why I call it an approximation. If you're going to test it, I advise doing so on a disk-image or on a USB drive that can be reformatted without losing anything of value.
Finally, I have no idea if schg or any of the other flags works on the server configuration described. Yet another reason for careful testing prior to use.