I think the idea that scientific code should be judged by the same standards as production code is a bit unfair. The point when the code works the first time is when an industry programmer starts to refactor it -- because he expects to use and work on it in the future. The point when the code works the first time is when a scientists abandons it -- because it has fulfilled its purpose. This is why the quality is lower: lots of scientific code is the first iteration that never got a second.

(Of course, not all scientific code is discardable, large quantities of reusable code is reused every day; we have many frameworks, and the code quality of those is completely different).