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You can already configure stall detection on extruders. See the M915 command.
Another solution is to use a filament motion monitor.
Thanks for the update!
What happens if you reduce the probing speed (F parameter in the M558 command)?
The probing move is terminated abruptly when the probe triggers, and if the probing speed is too high then it can overshoot.
I believe this issue is fixed in the 2.0beta series firmware. Bete 3 seems to be stable with no known bugs, so please try that version.