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Would it not suffice to just make the singletons "immortal"?
Without affecting the hotpaths that are Py_INCREF and Py_DECREF, changing _Py_Dealloc to test for objects with a "special" destructor could be used:
 destructor dealloc = Py_TYPE(op)->tp_dealloc;
 if (dealloc == _Py_SingletonSentinel) {
 /* reset refcnt so as to not return here too often */
 op->ob_refcnt = PY_SSIZE_T_MAX;
 }
 else {
 (*dealloc)(op);
 }
Even in the presence of multiple mutating threads, the object cannot be destroyed. Worst case, they all call _Py_Dealloc.