This is a little confusing to me; if the issue is the push notification why don't they simple stop doing the push notification? Or is it already too late for that?
I believe the issue has less to do with that than with capricious enforcement of rules, and little in the way of recourse for the victims of such.
If there were a formal review procedure with rules for when an app gets notified about scheduled future actions (and when those can be superseded when needed), as well as a procedure for fixing problems before negative actions (if there is it sure doesn't seem it's followed), then we would see less of these stories.
EDIT: The All Things D article sheds more light on what might really be going on here: http://allthingsd.com/20130408/confirmed-apple-kicks-appgrat...