If indeed the file is corrupt, you should repair your HD with Disk Utility or running fsck from the command line. Details here:
Apple Knowledge Base 106214
Note: ignore the stuff about problems with starting up; the procedure outlined is correct to repair corrupt files.
Use get info (command-I while file is highlighted in the finder) and make sure the file is not locked. If it is, unlock it by checking the box so the padlock icon is open.
If another application is using the file, a logout and login should fix that. Occasionally that won't do the trick, but a reboot will.
Once the file corruption is fixed and you have determined it is not locked or used by another application, you should be able to trash it & empty the trash.
There are also solutions by going into the command line, but before we do that try the above and the next method.
You may also try booting directly into OS9 (if installed) and looking for the invisble trash folder (filename begins with a period as in: .trash) inside your users folder. If the PDF is still on the desktop, then it will be in the users desktop folder. In each case, drag the offending file into the OS9 trash and empty the trash. If you still have problems, press the "Option" key and select empty trash.
If it still will not remove, then post back and we will tell you how to do it, for sure, with the terminal.