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.