I'm closing this issue because the behavior was addressed for Python 3 in POSIX and mostly addressed in Windows (PEP 443, bpo-19764). The switch to using PROC_THREAD_ATTRIBUTE_HANDLE_LIST with subprocess.Popen() in Windows at least makes scripts safe from race conditions as long as only the subprocess module is used. 

Eventually it would be better to use subprocess.Popen() to implement os.system() and, in Windows, os.spawnv[e] -- as was already implemented for os.popen(). In that case it may even be reasonable to use the handle list to implement pass_fds in Windows.