@dc42 This would be a great addition. I was doing a search for this feature, and this was the first Google hit. Has there been any progress on this feature since last year?
You mentioned controlling the deceleration. Is there a Duet command that stops steppers instantly? Marlin has a quickstop feature.
M410 - Quickstop - "Stop all steppers instantly. Since there will be no deceleration, steppers are expected to be out of position after this command."
PS: For those coming from Google. Here is another thread talking about how this would be helpful for clean jogging and microscopy applications.