Your criticism is valid from our perspective, but the non-software engineers on the other side of the culture divide are even less aware of proper software practice, so I don't see how the failure of software people to follow those practices could be the source of the prejudice.

I think it's a different problem. Software engineering is fundamentally about the management of complexity. People who have only worked on small programs -- like most non-software engineers and scientists -- don't understand the need to manage complexity because they've never worked on any program large enough to require it. Programming in the small is easy, particularly when you're mostly doing numerics. Other engineers see that and think that all programming must be easy.