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I just looked at subprocess in svs trunk and it looks like it might already be fixed in both subprocess.py and popen2.py. The part where __del__() adds abandoned Popen instances to _active and _cleanup() removes them is already there. _cleanup() has been made more thread resistant by catching and ignoring exceptions that arise when two _cleanups() try to remove the same instances. Popen.poll() has been made more robust by having it set self.returncode to an optional _deadstate argument value when poll gets an os.error from os.pidwait() on a child that gets cleaned up by another thread. I think there are still a few minor race conditions around Popen.poll(), but it will only affect what non-zero returncode you get... it's not so much "thread safe" as "thread robust".
I think the _deadstate argument approach to try and make Popen.poll() thread-robust is a bit hacky. I would rather see _cleanup() be properly threadsafe by having it remove the inst from _active before processing it and re-adding it back if it is still not finished. However, as it is now it looks like it is fixed...