feed a program an external script, looking for advice on high level approach.

not sure if Uno's Atmel chip that handles USB interface can be programmed for that.

I believe in theory in can, however the arduino IDE has no support for uploading firmware into the 8u2 chip, and if you changed it then you couldn't upload sketches as would normally done, so it would be an awkward feature at best. I think a shield based USB host device is a much more practical solution and I've seen one or two already offered: