You make a good point, which is why I edited my post to "more often irrational" before posting.
Fight or flight response isn't ever informed by rational/irrational consideration, because it wouldn't be an effective and useful response--it is a useful and necessary selective instinct and we know this because it is brain-stem level function (what we call "reptilian responses"--the part of the brain that all animals share--yes, even humans and lizards). For an effective fight or flight response, no thinking can be involved. It is purely reactionary, so you have a more or less equal-or-worse chance of running into greater danger in an attempt to flee, or marching towards death by decided to fight that bear. Yeah, sometimes you have no choice (can't get around that bear if you are backed into a cave), but we do know that the selection tends to favor those that intentionally avoid these threats--putting themselves in situations where flight/fight would actually be triggered. This argues that allowing oneself to be in a position to consider, and interpret, the consequences of a certain event is preferable to following a course that inevitably gets you trapped in a cave with that bear.
All of this is rather difficult to attribute to things like human interpretations of complicated political, geopolitical, social interactions. It sort of invokes the silly specter of "social darwinism" (a theory which, in no way, is applicable to the function of natural selection--a psychosocial designation that may be popular in literature, but isn't science).
The argument wasn't that "many refuges might be terrorists" and so that is OK--the argument is that the actual number--far, far less than 1% might be--and so that is OK. This is the same kind of risk we have always had when it comes to threats from immigration. Essentially non-significant. ...however, I don't like to equate the risk of a terrorist with the risk of something like traffic deaths or falling in your shower or even any other kind of random or targeted murder. I do think that the specter of terrorism and the risk of such has a greater effect on the population than can be determined by simple numbers.