It was obviously made for NSA. Otherwise the name wouldn't mention NSA. Microsoft didn't need the backup key, they were able to back up the single Microsoft key. Nobody designs the crypto with two keys accidentally. How NSA used it we can only speculate, but it was there on purpose, the truthful wording of Microsoft was "it was there for us to obey the law."
It seems reasonable that NSAKEY wasn't an NSA backdoor meant allow them to secretly install compromised crypto libraries on your machine.