I removed the Example Administrator account as per the Tech Note on the TAC site (Document ID 26846). This subscriber also appears to own the ch_defaulttemplate and be the message recipient for this call handler as well.
There isn't anyway of changing this via SA.
DBWalker complains about it but everything seems to work OK as far as creating new subscribers etc. Should I tell DBWalker to treat it as an orphan handler and delete it?
No, definitely don't do that... you need the template there which consists of the subscriber template itself and, of course, it's primary call handler. Just ignore the errors, the owner and recipient values are over written when you create a new subscriber with the template so it's not going to cause any problems. In 4.0 those values for the templates are forced to NULL so I'll be able to make dbWalker smart enough to fix the problem on the fly but in 3.x you should just leave it alone and ignore the errors.
If you're really annoyed by the errors you can fix this in DOHPropTest but it's not really that big a deal.