Y'know I have to agree. It's the one thing that has always bugged me about economics in general, and free market capitalism in particular. I mean sure one of the calculations made in Keynesian economics (at least according to my intro class) is the marginal pollution cost for any given action, but that in itself kinda bothers me. In a way it gives companies the incentive to pollute just as much as they can get away with and as much as necessary to accrue the greatest benefit (read: profit), when what we really need is a calculation that provides the incentive to pollute as little as possible, and have that hold the standard rather than the marginal return. Or failing that, a model that demonstrates that long-term returns are greater with less pollution despite greater short-term returns with more.
Note that I am using pollution as a catch-all term here, not to say it should be limited to overt industrial pollution.