Do you go to my university? :-)
What you're experiencing is a common, useful but sometimes anoying, feature of the Windows Installer (Windows Installers come as .msi files, but often have a .exe file to launch them). The Windows Installer has a healing feature that checks for things being moved around, deleted, or corupted and "fixes" them. It certainly is not isolated to Symantec Endpoint Protection, but any software using the "healing" features of the Windows Installer.
Odds are the executlabe file you're getting could be extracted via a program like
7-zip (a nice freeware archive manager). Once you do that, you probably can find any scripts they use to install the program or may find that it was just running the MSI directly. Depending on what exactly they did, you might be able to change the installer's behavior, but I can't be specific not knowing what your University's IT staff may have done.
If this request came accross my desk, I would have provided you an installer that didn't cause these problems--but I'm a few layers behind the help desk people. Have you tried to escalate your request?