Sure it's safe. Just make sure they're properly capped so nothing is going to short against anything else (including the controller casing and bike frame). And make sure you either leave enough of a stub to solder/crimp a wire back on if you ever decide you need the functions you've cut the wires for. Or just be really sure you'll never need those features. I suppose you could just open the case and resolder a new wire inside in a pinch.
Again, make sure they're well covered, I usually use short pieces of small diameter shrink tubing, and pinch the open end shut while it's still hot. Sometimes this hurts a little. I should find another way. But it hurts less each time I do it.