If you captured and replayed the IR flashing signals you might be able to abuse such a system to prevent people from taking pictures of other things, such as yourself. I wonder if a little bit of cryptography embedded in the signal and the phone could make replay attacks more difficult, perhaps something similar to the codes used by garage door openers and car keyfobs. Or maybe by encrypting a counter.

If the IR sensor was separate from the camera module you might be able to put tape over it and prevent the signal from being received by your phone, defeating it. But if the IR sensor was actually a custom component embedded inside the CCD chip (which is not out of the question for Apple) then this would be difficult to defeat. You'd have to carefully mask out the non-IR-filtered area of the CCD chip with material that filters IR.