I haven't found anything to work outside of "erase all content and settings" or restoring the phone via itunes
One thing that seemed to prevent it from happening in the first place though is to monitor when your phone is downloading the update via settings > general > usage and if it has started downloading but hasn't finished yet, delete the update before it finishes downloading completely and you won't have a badge on the settings app.
It is annoying to look at though.