IR filters can only attenuate incoming IR so much while still allowing nearby red wavelengths through. And any filter will have a non-flat response through the visible wavelengths, slightly distorting the color response of your photos.
A properly coded IR signal from the transmitting 'disabler' device could still be picked up by the iPhone even if it was severely attenuated. At ~30fps, you can quickly get 100+ samples to cross-correlate with to search for the encoded 'disable' signal.
My gut feeling is that Apple patented this technology because it was low-hanging fruit. They saw they could roll it into a legitimate patent and prevent others from claiming it down the road. Still, I think it's worthwhile to send a quick letter to the powers that be to let them know we all disprove. If it does get implemented, the popularity of jailbreaking will move up another notch.