Most of us simple do what we have the habit of doing. None of the methods are "wrong". You will see huge debates over using the kill switch, with people quoting from various places that it's for emergency use only. What ever. It's there, it's part of my routine to use the kill switch. It does the intended job.
In regards to turning off the ignition, isn't that what we all do for every car we own? No harm that way either.
Essentially, there is a circuit with several switches in it. Break the circuit, the engine dies. Side stand is one of those circuits. If the engine dies, the rest of the system is still live, same as if you hit the kill switch, so you have to follow that with the key switch to turn off the power. Sort of like turning the key on a car from run to acc, the engine dies, but the system is still live until you turn the key the rest of the way to off. Again, no harm there, it's just not 'off' until you turn it off.
So pick your poison and enjoy your riding. If the kill switch wasn't there, you wouldn't ever try and start the bike with it off.
I figure it's there, so why not use it. I haven't forgotten to turn on the kill switch in about 25 years, perhaps because it's my habit to use it every time.
Either laugh when your friend tells you that again, or ask him why he believes it could cause a problem, and on how old of a bike did he experience that problem himself? If he never actually experienced that problem himself, laugh again and tell him to stop believing everything he hears or urban legends.