So one of the many services the NSA offers to the US Government is reverse engineering. Do you really think that his software was so mysterious that they couldn't figure this out eventually?
That's resource intensive. They might have, but it's also entirely possible they would have decided it wasn't worth it. Might as well first see if the author is kind enough to just hand over the source. At the very least, he should have made the code open source after giving it to the NSA so that there was a chance of zero days they discovered getting worked out.
> They might have, but it's also entirely possible they would have decided it wasn't worth it
That's an enormous assumption based on zero evidence. The only resource the NSA is limited by is time. Money and man power (up to diminishing returns) are effectively limitless.
They were trying to skip a step, but there's absolutely no reason to believe they could have (and would have) done without through reverse engineering the binary. The NSA guy implied time was the major factor, and wanting the source certainly implies that was the case.