Sophos Clean needs activating the first time it is run on a computer. Doing this across multiple computers is going to be a pain in the butt. Thankfully, help is at hand. Or foot. If you're an alternative life form reading this, then tentacle is also available.
Sophos Clean has multiple command line options for automation purposes. I'll come to those in another post. The parameter we're interested in right now is /LIC=
That is used to apply your license key e.g
Use your current automation tool - GPO , LANDesk, ZENworks, SCCM or whatever to run sophosclean with that parameter. That's enough to complete the activation process.
Note: The device will need an internet connection.