We're not pulling the data from the fed site, so there is no issue with the use of that data. We work with a group that maintains this data independently of the published fed directory.

I am also interested about this. I hope someone with enough legal background chimes in here.

Could the company claim that they are providing a service of programmatic access to that data? I mean there is added value here, so I don't see anything particularly wrong here, ethically speaking.

Well if they're charging for the service which uses data which says "The information contained in the directory may not be sold, relicensed, or otherwise used for commercial gain", it's hard to argue that they're NOT doing just that.