I tried out a simple change (to the trunk) in _PyModule_Clear to prevent this particular problem.  Between the "remove everything beginning with an underscore" and the "remove everything except __builtins__" steps, I added a step to remove all instance objects in the module's dictionary.  It appears to stop this problem and passes the regression test suite.  I can post it as a patch if this seems like a reasonable change to make. 

Also, I noticed that earlier I posted the wrong link for the location of the example code; it should have been:
     http://www.dpawson.co.uk/bop/byteofpython_120.txt