But externalities have no inherent or obvious cost to market participants, either because they are so distributed that the cost per participant is ignorably small, or because the costs are distributed in time (and thus do not affect current market participants) (or both).
The cost of externalities has to be determined and that inevitably involves questions about values. As a trivial example: how much do you (or should you) value clean air? What ppm contamination is worth a dollar to you every time you purchase fuel?
This means that a "free market" with prices that include the cost of externalities must inevitably be regulated in some important sense, since the cost of externalities can only be established via the same processes used for regulation in general. And by most definitions of "free market", that is no longer a "free market".
That doesn't mean this isn't the right thing to do. It just needs better terminology to describe it.
I agree. The externalities should be accounted for. Petroleum should be taxed and not subsidized.