Basically, what do you think the immune system in somebody with a bee allergy is actually doing when that person gets stung by a bee? It's only trying to help, of course. But that doesn't change the fact that 1) a bee sting can be ignored and 2) the massive allergic reaction threatens the person's life.
Also, don't underestimate terrorism. Over decades, the IRA did a lot to disrupt the UK, including killing cabinet ministers, and two nearly successful assassination attempts against the prime minister. Ultimately the UK conceded and the new Irish government contained ministers who had been leaders of the terrorist movement.
As far your IRA example, the US doesn't face anything like that, and shows no prospect of doing so. Even if it did, I'm not convinced that efforts like the NSA's would be very helpful in combating it, and given the example of the last 12 years, I'm quite sure that the US government's reactions as a whole would be far more damaging than the terrorism itself.