Have you tried rm -f? Or maybe try having the user logout and back in and then run the command.

Yes. I've tried rm -f. I haven't tried having them logout and then run the command. It's difficult to test because i can't replicate the problem exactly how it happens to them. I can only open a file on one computer and then open the same file on another computer with my test network account.

You could also try moving or renaming the entire "Adobe InDesign" folder and then delete the moved or renamed folder at login or the next time you run the command.

Could also try clearing their Adobe cache at login or include it in the command as well.

I think moving the folder will be the solution for me. It allows InDesign to create a new folder in its place. I still can't delete the renamed folder, but maybe i can be deleted on login the next time like you said. Thanks!

You can also teach the shortcut, add it as a custom item in Self Service, etc:

While pressing Shift+Option+Command+Control, start InDesign. Click Yes when asked if you want to delete preference files.

http://help.adobe.com/en_US/indesign/cs/using/WSa285fff53dea4f8617383751001ea8cb3f-6d21a.html#WSa285fff53dea4f8617383751001ea8cb3f-6d1ba

I should have mentioned that this did not work. Probably the same reason rm doesn't work.

That doesn't surprise me. If you can't rm a file/folder, you usually can't move/rename it either.

I'm a little confused. In your OP above you state:

The solution to this is to navigate to ~/Library/Preferences/Adobe InDesign/Version 9.0/en_US/ and trash the file 'InDesign Defaults'.

But then you mentioned needing to delete a file on a share point path. When you navigate to the user's home dir to delete that file, is it actually in the path of /Network/server/user/path/ etc…?
I'm just wondering if there's some local path on the Mac this can be deleted from instead of on a home directory sharepoint?