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Ok, I think I've managed to dig to the core issue. It is actually the same issue as https://bugs.python.org/issue11768 (which was wrongly closed as fixed, apparently :-)).
Py_AddPendingCall() calls PyThread_acquire_lock() to try and take the pending calls lock. Unfortunately, PyThread_acquire_lock() is not reentrant in the case where semaphores are not used (e.g. on OS X). We can probably fix that first issue by calling pthread_mutex_trylock() instead of pthread_mutex_lock().
There is a second more fundamental issue, though, which is that PyThread_acquire_lock() calls into functions that are not async-signal-safe (see http://man7.org/linux/man-pages/man7/signal-safety.7.html for a list). So, depending on the particular OS and libc implementation, PyThread_acquire_lock() can fail in mysterious ways (including hang the process) when called from a signal handler.
So perhaps the ultimate fix would be to remove the OS-based locking in Py_AddPendingCall and use a busy spinwait... The performance implications may be bad, though.