I haven't re-read the 1KRR manual for detail, but in my F4i manual it specifically said to not use the kill switch to turn off the bike, so I don't on my 1KRR either.

A friend of mine sat on my 08 the day I got it, and he turned off the kill switch. He went back to start it later and no dice. Took a couple of minutes (with me freaking out) before we figured it out. Been there.

<edit> I just went and checked the 08 1KRR manual, and it's worded a little differently than what I remember in my F4i manual. It just says that the switch is an emergency switch, and should normally be left in the RUN position even when the engine is off. Doesn't give any reasons.