Ex-religious Jew here. This is a bit of a mis-characterization (though an understandable one). For those who believe the Torah is the infallible word of God, with laws meant to apply universally through the ages and maximize human benefit, then two things must be true:
1) everything, even apparent loopholes, must be included intentionally, and
2) these laws must be formulated in a way that's flexible enough to conform to changing realities, while sturdy enough not to devolve into ambiguity.
The case of the Eruv offers an example of exactly that.
You're right, that the original commandment, as stated, is pretty clear. Carrying outside of (or between) private residences on the Sabbath is prohibited.
The Sabbath is meant to be a day of rest, so the restriction on carrying things to and from anywhere outside of your home would all but force families to stay in-doors, with each other.
BUT... if the demands or realities of a different (i.e. less than ideal) time were to change so that such an arrangement placed too onerous a burden on worshipers, then the law has an escape clause.
Through the incredibly meticulous and tedious construction of a sprawling boundary, any space could become technically "private."
The rationalization would be that though this was a loophole, the sheer difficulty of exploiting it would signal that practitioners of the Sabbath (and especially the Rabbinic authorities needed to approve and supervise an Eruv) literally had no other option than to sidestep the commandment as originally intended.
It's worth noting that relatively few Jewish laws have such escape clauses.
The thinking is that it signals only those laws for which ideal circumstances are required to actually observe them. To be clear, the original commandment always holds (because even when you do construct an Eruv, let's say, you still must have the original commandment in mind), but there is a threshold after which observing this stricture in a surrogate manner is deemed acceptable.
The only book of Pinker's I found useful was his guide to writing called "A Sense of Style." This columnist could really benefit from giving it a thorough read.