You should be able to use "accessibility" features to bring up a soft keyboard (or just cut and paste from known things) to run the entire attack as a normal-appearing HID mouse, which just happens to be evil. No need to reconnect via a hub; you could do the whole thing within a mouse controller. Bonus points if you can manage to fit all the logic in the same processor/memory the thing includes by default, or something which looks like the same physical package and thus passes a non-destructive open-device analysis.
(which is kind of terrifying if you think about it; almost no one checks the provenance of "dumb" devices like mice. Keyboards sometimes get a tiny bit more scrutiny due to hardware keyloggers inside inline, but that's about it.)
The ultimate solution is a trusted supply chain and equipment which is tamper-evident, non-counterfeitable, and which can securely attest to intactness and provenance; x9.9 pinpads and hsms. But no one does that for general purpose hardware.
The environment I'm thinking about is something like a SCADA control system for, say, a centrifuge cascade :)
How hard would this part be?
> But surely you could simply test the hardware
Scanning system devices would reveal it pretty quickly if it's just an additional USB device.
It's not hypothetical. A friend of mine has created an USB based pen-test tool based on this very idea. The early prototype idea was to open up a mouse, splice a USB hub into the USB connection, then attach an "Arduino like" Teensy[1] to it such that, when the mouse was connected, in addition to the mouse being detected and registered by the host machine, it would also detect and install a new keyboard. The Teensy could then dump it's payload as anything that could be typed on a physical keyboard (subject to the memory limitations of the board).
He's now doing a Kickstarter campaign to manufacture and sell the things, which he calls The Glitch[2]. You can see pictures on the Kickstarter page, of the Glitch embedded in a generic mouse.
[1]: http://www.pjrc.com/teensy/
[2]: http://www.kickstarter.com/projects/1186217328/the-glitch