If I were Apple I would make the IR processing happen at hardware level (so no jailbreak) and I would make sure the hardware would stop working unless a physiological level of background IR light is picked up.
That means that an IR filter physically placed in front of the objective would stop the secret signal but make the camera useless as well.
Besides which, when Apple adds features, they traditionally do so to benefit their users. I'd suggest that, even though they cite concert censorship as an example of use in the patent, that's probably a cover-all-bases addition; we're more likely to see an iPhone IR sensor that enhances the user experience rather than one that impedes it.
That means that an IR filter physically placed in front of the objective would stop the secret signal but make the camera useless as well.