Well a relatively simple solution would be to run ClamD as a remote service. That way, you can configure it however you like and SmarterMail upgrades won't affect it. (I say "relatively simple" as that is kind of subjective.)

I did ask the devs about this, and when SmarterMail updates a number of those settings are configured during the upgrade. TCPAddr and TCPSocket may or may not be required to be updated, but they are anyway just to ensure that SmarterMail can talk to ClamAV, at least in a default configuration. (Which, I'd say, is probably how the vast majority of people run it.) What I'll do it put in a request that the devs discuss that process -- perhaps we can avoid overwriting those particular lines.