I don't pretend I know what happened to your bike, but I know that when my jetting is right on the money, or a little lean, my 2 strokes will run away when coming off a high rev with no load. They'll scream until you load them or kill the ignition. I've seen it on my snowmobile, motorcycle and my boat. My boat, a 200HP Merc Black Max has a factory ignition kill box on it for that exact reason. If the vacuum goes high it kills the spark until it idles.
If I had to guess, I might think that the pipe leaned it out, you had a no-load run away and just got a little confused about the kill switch and clutch not working during the panic. I'd check my jetting to be sure it's not too lean before putting too many hours on it.
Good luck,
Joe