Quick update on this topic: I was able to modify the height following code to control the speed of any axis based on analog inputs. I was able to use it to print with our six-axis robot and initial results seem promising.
If ever this might be useful to someone, the code is here: https://github.com/soccerpaul/RepRapFirmware/tree/3.3-dev-analog_extrusion. I've currently just replaced the height-following files with mine instead, but it would be pretty easy to modify them to make them compatible with the main reprap firmware branch. I may try to do this in the coming months.
One last question: I was never able to use the height following code at more than 50Hz, despite the code indicating it should work up to 200Hz. For standard height following, motion becomes very erratic beyond 50Hz and the z-axis won't hold its position correctly. Using my modified code, motion becomes extremely jerky beyond 50Hz. Is there something that somehow limits the frequency of the aux move queue?