IMO, removing the auto decompression lever would be a mistake.Without it in place and operating as it should, the starter motor, starter gear train and the sprag clutch will be subjected to much higher loads as they raise the piston against the full compression caused by the exhaust valve being fully closed.This sounds like a good recipe for part failure to me.
Can you be a bit more specific about the noise it was making? Was it a tappet-like clatter, and did it begin suddenly? Was it much worse when the engine was warmed up to full operating temperature? Was there metal coming out on the drainplug magnets?