I guess you are referring to the fact that if we kill the engine with the switch, the battery still powers the capacitor/ignition coil which might give way if the engine is not running ( was told to me by a car mechanic for my Maruti 800). even if that is true, I would still say, that the damage is limited to the coil and not to the engine...when we say engine then I mean piston,head,valves,cam,timing chain, con rods etc.

anywhichways, I am sure, Engine kill switch harms the engine...thats the reason why My Zma does not have one.......(ok I was being sarcastic now!!)

It does no harm. U can safely use it.

If u are talking about the R15, some guys even mailed Yamaha and got their doubts cleared. Yamaha said that we can use it as often as needed.

Query Approved.

I remember reading something like this too, vaguely. I do not quite know whether it is harmful or not if used excessively, but I anyways use the ignition to switch off the engine totally, while in a traffic light. It is a habit actually, which is in me mostly because of the Pulsar 180 which I used to ride before my current bike (the Pulsar 200).