I don't think people were attacking "you" personally...They are attacking the issue of engine braking or not.
The irony of this whole thing is, as "The Big Red One" put it......Most people that have been around bikes for a while already know this, and it's shocking to think that there are people will little experience out there on one of the most powerfull production bikes. As he said; most of us assume that others have worked their way up to the Busa, and not just gone out and bought a shiney new toy because we had the money.
The learning that most long time riders experience, is one that teaches you what to expect from a bike, and how to feel the bike's handling. This experience helps you to make sound decisions based on experience and knowledge. Without anything backing up your decision process, the decision you make may in fact be your last. For maximum braking effectiveness, you do in fact need to use your gears, but then there's a catch...
As you really stand on the front brake, the weight of the bike is shifted forward. This reduces the pressure applied to the rear tire by the suspension. This reduces the available contact patch and if you downshift too aggresively, or attempt to apply the rear brake, then the rear tire is going to lose traction and cause a skid. Do you know what to do during a skid? Have you practiced it recently? Try doing it from 160 mph coming down the straight into a turn. Holy shid is that fun...scary, but fun.
If the rear brake is modulated and the clutch feather during this emergency stopping, then it will only add to your stopping power. It will not hurt the bike or the engine. You can cause damage by gearing down too aggressively though.