Once you get the mechanical problems sorted out:
Tell the stoker to give you a kidney punch any time you start pedaling too fast or for any other violation of tandem buddy courtesy.
Persuade the stoker to try foot retention again.
For the first few rides once your stoker is again willing to ride with you, go for much shorter rides far from traffic and hills.
Your stoker will probably eventually ask to resume the longer rides.
All this assumes that you haven't permanently burned that bridge.