I would get back on the phone with McAfee and point them to this post.
Demonstrate to the L2 how the file isn't deleted when real time scanning is turned off. You can prove this by starting and closing iTunes several times for them with real time off.
Then turn on real time scanning and typically on the 2nd or 3rd re-start of iTunes, the file is removed (you may need to hit refresh to see this).
Also, technically, the file isn't deleted, at least not in the sense like you manually deleted a file, because the file isn't placed in the recycle bin.
I would also have them demonstrate exactly how McAfee would prompt you if it were going to delete a file. Sounds like a line of BS to me, because McAfee would place the file in quarantine first (problem with McAfee however is that you are not prompted when it has quarantined a file, bad design IMO).
I also uninstalled McAfee, and run the McAfee Removal Tool (to make sure McAfee was completely removed, per this link: http://service.mcafee.com/FAQDocument.aspx?lc=1033&id=TS101331
Once McAfee was removed, I had no problems with iTunes, (settings saved as expected).
I reinstalled McAfee, and the problem with the iTunesPrefs.xml returned
McAfee should be able to determine that it's an issue in real time scan pretty easily.