Would it be okay to do a check on __index__ after the PyLong_Check() succeeds?  Something like this:

    if (PyLong_Check(item) &&
        item->ob_type->tp_as_number->nb_index == PyLong_Type.tp_as_number->nb_index) {
        Py_INCREF(item);
        return item;
    }

This is something Nick and I were talking about at the sprints regarding fast paths in the abstract API (for mappings and sequences in our case).