Thanks for the background information.
Have you looked at our Multiple Signatures (http://advansyscorp.com/formativ_sol_multiple_signatures.htm) solution? It lets you to create and choose from several signatures, define a default signature (plain text or HTML) to be automatically inserted when you run the solution. You can also integrate the solution with Message OnSend event then disable the GroupWise signature, so the personal signature will be added when you send the message.
All Advansys solutions provided as free, fully featured 30-day trial software. Please feel free to test the solution to see whether it meets your requirements.