You can either cut the shaft off just beyond where it extends out of the seal, or you can open the engine up, cut the crank off just beyond where it extends through the bearing, leave the seal out, and then use something to seal off the back of the crankcase. Sometimes I do it one way, sometimes the other; it depends on my mood that day I guess.

I have used flat pieces of aluminum to seal off the back of the crankcase, and I have used automotive freeze plugs pressed into the recess where the seal went. You lose a touch more weight cutting off the crank inside the case, and also lose a potential leak point and the seal drag. But there is nothing wrong with just cutting it off just outside the seal and leaving the seal. Just make sure you don't get the crank hot enough while cutting to damage the seal.

AV8TOR