This thread can be closed. I found the reg key it adds for starting up the Outlook add-ins, so am modifying the install script to add the key with a different value for the load behavior.
Anyone wondering the path, it is:
Computer\HKEY_CURRENT_USER\Software\Microsoft\Office\Outlook\Addins\WebExOl.Addin
Change the "Loadbehavior" value from 3 to 0.