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Using any kind of potentially-blocking synchronization primitive from __del__ or weakref callback is indeed a bug waiting for happen. I agree non-trivial cases can be hard to debug, especially when people don't expect that kind of cause.
It would be ok to submit a patch solving this issue using C code IMHO. Note the maxsize argument complicates things even though most uses of Queue don't use maxsize.
Of course, the general issue isn't only about Queue: other synchronization primitives are widely used. See https://github.com/tornadoweb/tornado/pull/1876 for an example.