It should be absolutely safe. Whether it behooves your complete setup or not, that can be determined by someone more in touch with these engines, along with you listing your other modifications.
But I vote for letting it ride. I'd sacrifice a little power in the name of packaging on a mini bike. It should still be more powerful than your stock muffler; and chasing tenths of a horse is something best left to racers, bench or otherwise; IMHO.