Since the beginning of engines grounding out the mag is the way of killing the mag it gives the current some place to go into, the frame, it will not hurt the mag or its systems, popping off the plug wire will do more harm if the plug wire can't discharge it's energy like its supposed to then it will fire its current possibly right out the side of the coil.
battery ignition's systems interrupt the flow of current.
choking the engine to stop is flooding it so bad that the spark plug can't fire. Gee Wally why isn't my engine performing so good and my plug is fowling out crumby ol china plugs. How many times have we heard that?
So go ahead and stop your bike how ever you want to.
I'll stick with a kill switch its saved my son a nasty wreak or a blown engine if he would have pulled in the clutch when the throttle stuck.