Though there are some situations where it is nessacery. Consider vtund for example which has seperate enable/disable flags for running in server and client modes (with the potential for multiple seperate client instances).Many packages seem to provide ENABLE/DISABLE variables in /etc/default/foo, providing a confusing red herring for this task --- a second method which does not work nearly as well, as you pointed out
A complicating factor is that the sysadmin may already have customized some ENABLE/DISABLE settings and a move like this should not override their settings. So perhaps packages should stop advertising the ENABLE/DISABLE vars in /etc/default/<package>, but continue to respect them when set.
regardless of any plan to discourage use of the /etc/defaultmechanism (I think removing it altogether is not really reasonable) I think the original bug of being unable to stop a dameon after disabling it in /etc/default still needs to be fixed.