The way I understand it, the FAA checks to see if the software design was designed and tested according to documented procedure, which was approved beforehand. The procedure must follow some published guidelines, mainly [DO-178B](http://en.wikipedia.org/wiki/DO-178B). The FAA person probably doesn't need a CS degree to check this. They just need to be competent enough to review the documents generated during the DO-178B process, and see that they did what they said they did. The civil liability I think would come in if a company forged their documentation. And if the documentation is not good, then the software won't get approved by the FAA audit. At least that's how it's supposed to work.

Edit: There are third party or FAA technical experts involved, so I guess your point still stands. But I don't think certification can replace this kind of following engineering procedure. And yes, I consider software engineering for safety-critical applications an engineering discipline.