The “danger” is there because “do this at your own risk” and to open discussion on it.
The common wisdom is to turn off power prior to swapping the Y-Axis and rotary steppers. As I was responding to a different thread, I dropped in the “turn off power” comment. You don’t want the back EMF from the stepper to toast the driver.
I confirmed that the stepper drivers are still enabled even while idle, but if they were disabled there wouldn’t be power going to the steppers and there would be no back EMF problem.
On my machine, the enable pins aren’t connected on the drivers, so the steppers are always enabled.
So, you could push-button activate a latching/toggle relay to swap the axis wires after a delay to drive the enable pin low (disable). No need to power down.
I also wonder if you could use the Run signal (maybe inverted) to drive the stepper enable. I need to see if that’s on-while-moving or only on-with laser. There is the possibility of losing a couple of steps due to timing,
My ideal state would still be able to use one of the general purpose outputs and Lightburn ability to toggle them for rotary. Last I heard, though, the outputs aren’t actually accessible. 
“Things to check, things to do…”