Releasing the GIL when calling C library functions (e.g. opendir()) is not a requirement, it's just an optimization for slightly better multi-threading. Also, as shown in the backtrace, PyGILState_Ensure() is called which should only try to acquire the GIL if it isn't already held by the current thread; that is, it is designed to avoid the deadlock you are witnessing.

So, I would suggest the problem lies somewhere else. Does FUSE implicitly do a fork() of the current process? It's not obvious how the example shown here works.