Could missile targeting be assisted by someone on the target, such as a passenger with a small, low power homing device? What if, just for the sake of argument, Homeland Security knows about a different kind of terrorist event planned for the holidays and that’s why they’re plying hardball on inspecting even toddlers. I’m not saying it’s so, and I’m sure not saying the ends justifies the means, but the Israeli security model is built on the assumption that the terrorist inflicting the damage will be in or close to the aircraft at the time of detonation. What if we have intel suggesting a whole new model has been developed that doesn’t require an in-person trigger-person? Suppose that, well away from the airport, a terrorist gives a child a piece of candy with an altitude triggered signaling device used to guide an otherwise inaccurate missile directly to its target? If our intel hasnt caught up with the terrorist ground units, how would we defend against an attack like that, other than, as you say, countermeasures from the plane itself, be it evasion or otherwise?
If they have ground-to-air missiles in this country already, the chance to stop them has already passed us by. No matter how many people the TSA gropes.
As ex 98C MI Dude already mentioned, MPADS don't have such a function. The reason is quite simple: it is highly improbable that an enemy aircraft will have one of those beacons handy. But there are a few laser-guided missiles (Swedens RBS-70 and Britains Starstreak.)
In this case the passenger jet already is equipped with a few very powerful beacons; they are called "engines" and they are as bright as Sun to the infrared sensor of the missile; they are plenty fast to be fired in the "tail chase" mode and catch up with the target.
There were several MPADS attacks on civilian airplanes (see the link.) Out of eight attacks seven resulted in hits, and one miss is attributed to the wrong (training) missile being used, as it had no guidance system. In other words, an MPADS attack is most likely going to end up in a shootdown.