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I agree that this behavior wrong, this should only trigger an error when building packages.
How did you build python? I guess something like this:
$ export MACOSX_DEPLOYMENT_TARGET=10.5
$ configure --enable-framework
$ make install
This should result in getting the right deployment target into config/Makefile, which means there may be two bugs here:
1) sysconfig.get_config_vars shouldn't trigger and error, only 
 the distutils build command should do that
2) config/Makefile should always contain the value of MACOSX_DEPLOYMENT_TARGET as used during the build, which in turn should
mean the value during the configure step.
BTW. I tend to configure like this:
$ configure --enable-framework MACOSX_DEPLOYMENT_TARGET=10.5
That way automatic reruns of configure pick up the right environment variables.