[Andrew]

Steve, since the clippings Mail bundle (OmniMailMessageServiceEnabler) lives inside the OmniFocus application, Finder won't let you trash OmniFocus while Mail is running if you have installed the OmniFocus Mail Clip-O-Tron 3000 from the Clippings preferences pane in OmniFocus.

If you quit Mail you should be able to trash the old copy of OmniFocus, then restart Mail (probably want to do that after installing the new copy of OmniFocus). Note that the new copy of OmniFocus needs to be installed in the same location as the old copy or the OmniFocus clippings Mail bundle won't be found by Mail, and you'll have to re-enable it via preferences.

And no, this shouldn't be able to cause any kind of corruption.