I don't have any opinion on whether this issue kills the "parallelism with sub-interpreters" idea (I'm not sure why it would). But regardless, solving this issue will be very non-trivial, or perhaps very involved.

Running the GC at the end of a subinterpreter certainly won't solve the general problem of objects becoming unreachable in an interpreter (i.e. the last external reference being lost in that interpreter) and collected by the cyclic GC from another.