While I agree its best to avoid overlain axes like this, it is sometimes useful and standard in various scientific fields. Plots like the second one in
http://dusk.geo.orst.edu/gis/student_bibs/wingard.html are so common in my field that you would be looked at askance if you didn't produce this. Sure, you
could use seven panels instead of 2, but if you wanted to get it on one page and be able to line things up in the vertical, you'd have to sacrifice the resolution of the wiggles. For this data, a little bit of confusion and complexity is well worth it to be able to see the fine and important detail that smaller plots would obscure.
Note the authors here aren't trying to imply correlation. Its raw data. They are using these plots to
search for correlations and patterns. When you are doing that it is very useful to overlay plots. In the old days, folks used to do this with light tables. Maybe OmniGraph is only meant for publishable results, but there are other uses for plotting software than plotting final results.
In all, the article comes off as pretty prescriptive, and frankly it seems that whoever wrote it has never analyzed data seriously. You can say that you don't want to program double y axes, or that it isn't technically possible, but I'd sure stop far shorter than you do of claiming folks aren't using overlain axes properly. There is a reason you get a lot of request for this, and its not that your users are bad at analyzing data.