I'm not an expert on syncing, so I don't know if there's a way to remotely delete data. I expect that "Unregistering" a client, or changing a password for the WebDAV server would only mean that the remote copy of OmniFocus would be unable to continue to sync. The local copy of the database and software would still be there. Can you force a sync on your remote computer? (Showing my ignorance.) If you could, then you might backup your database, clear it, sync the remote computer (so the database would be empty), and then Unregister the remote computer. Then restore the database on your own Mac to the backup....
The best thing that I can think of to protect your data is encryption. (I do have experience with this - company policy, in case of theft, snoopy people, etc.) If you do have FileVault enabled at work, then all of the data in your home folder would be encrypted, and therefore inaccessible. If you don't like FileVault (wouldn't blame you!), or aren't allowed to use it on office computers, or are concerned that people may try to exploit FileVault's vulnerabilities to access your OmniFocus database, could you put your database in an encrypted disk image? Just don't put the password in your keychain.
Another possibility - has anyone been running OmniFocus with their data on a flash drive?
And another question: If this is about laying people off because of the economy, is your employer so mean-spirited as to say "Leave right now and never come back", or might they give people a little bit of time to collect personal items (your Starbucks Amsterdam mug) and personal data (your OmniFocus database) before going? Perhaps you should start making an OmniFocus project that will remind you of all the details you need to take care of at the office in the event of being laid off.