If I take the engine apart, then I just chuck the crank in my lathe and use a parting tool to cut off that back portion. I usually cut it off just past the rear bearing. Then you can make an aluminum block off plate for the rear shaft area, and do away with the seal. This eliminates not only the weight of the rear shaft part and the seal, but also eliminates one more possible leak area; the rear seal. It also probably increases power a bit, both due to the decreased crankshaft drag, and the decreased crankcase volume...

However, if you really don't want to take the engine apart, then yes, you can cut off the crank piece with a cut off wheel and a dremel. After the first few thousandths of an inch, the cranks aren't as hard as most people think. Just go slowly and make sure you don't overheat the shaft enough to damage the seal. If you end up with a leak there, it will drive you nuts....

Have fun,
AV8TOR