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I like #2. I don't see any use for threadsafe Popen instances, and I think that any self-respecting long-running server using Popen should properly manage its subprocesses anyway. (And for short-running processes it doesn't really matter if you have a few zombies.)
One could add a __del__ method that registers zombies to be reaped later, but I don't think it's worth it, and __del__ has some serious issues of its own. (If you really want to do this, use a weak reference callback instead of __del__ to do the zombie registration.)