The best you can do in that instance is to code it (and bill it!) as a 'customization' that is maintained separately from the core code. That way code to satisfy the cranky customer doesn't have to affect (infect?) your other customers' experience.
Maintaining code branches is its own nightmare--far worse than including it in the main code, in my experience, since you have to backport all future fixes in some fashion.
Then you have to maintain the plugin interface. It is usually better to just use a hidden setting (see about:config in Firefox) to control access to these things. K.I.S.S.
