marble sawmill

Interesting idea, I had forgotten about external offsets. This might offer a way to move the z-axis from hal while gcode execution is on feed hold (presuming feed-hold and feed-inhibit pins do not apply to external offsets)

[edit]
Just tried it and external offsets are indeed not affected by feed-hold and feed-inhibit pins. 
So this may give you the hal tools needed to stop gcode/mdi execution of y-axis movements and raise the z-axis up to the safe height. You would then need to think about how to proceed from there. Just issuing a program stop will still leave the operator to deal with the applied external offset.

Maybe wiring in hal so that stop would also trigger offset reset, when mode-is-auto pin goes false?

That would be the ideal solution, unfortunately it does not exist yet. That would need a modified interpreter which I have not looked at doing.
Alternatively, checking a gcode program at load time can be done by examining the line segments of the preview. That is what axis gui uses to check for limit violations on program load and I have modified that before.
The bigger challenge would be filtering the MDI command entry in the gui as you would have to examine that before it gets passed to the interpreter. Although being in python world it seems quite possible. In your case it should actually not be so difficult since you could simply reject arc moves instead of having to calculate way points to check if a G2 or G3 move would take the machine over a limit.

[edit]
Mind you once you start to introduce work and tool offsets things are going to get very complex very quickly.