Externalities are not a problem when all property is owned privately and the courts are philosophically equipped to handle the ordinary disputes that arise.
Remember that if you can detect some pollutant or annoyance well enough to write a scientific paper, you can probably convince a court, and there is probably a big enough market that detectors for the chemical or vibration (or whatever) can be sold, making effective, objective litigation (inherently a nonviolent process) much easier. This works for land, sea and air.
Interestingly, the way to overcome this problem is to develop and use combination therapies. I learned (in a virology class, but the principle applies to anything with a replicating genome) that a very good estimate of the combined resistance rate is simply the product of the separate resistance rates associated with each drug in isolation. I don't think this is commonly done with antibiotics yet, but perhaps someday this will become necessary.
I should also mention that when the selective pressure imposed by an antibiotic is removed, a population of resistant bacteria will invariably revert to a wild-type phenotype because of random drift (or loss of its resistance plasmid where applicable). So old antibiotics do become useful again after enough time passes.
Antibiotic drug development essentially ceased in by the 1980s for a bunch of complex reasons - breaches of capitalism as well as scientific naivety - I think that we'd be just fine right now if the pipeline had not stalled.
More fundamentally, capitalism needs more than just an economic defense (plenty of people and organizations do that today, and while their arguments are essentially true, they are not going to win that way). Capitalism is the only moral social system because it is by definition the only one that is compatible with individual rights. Individual rights are required because only reason allows mankind to maintain the conditions required for his survival. Any other system or "tweak" necessarily requires the initiation or threat of non-retalliatory force upon innocent men, which necessarily stops their minds in a manner proportional to the degree and scope of the threat.
The next step is pretty simple - what is the good? The altruistic idea of the good is not logically sound; if the good is defined as helping others, how is the good defined for the recipients of that help? To tack on another rule to solve the conundrum isn't sensible - to morally bifurcate humanity a priori (in this case, without looking at the specific actions of a particular person that arise from free will) should give you pause. Rand's answer is that every human being exists for their own sake, and that the good is what is in their own long-term rational self-interest. This is a precondition for proper and healthy human relationships; to the extent that people pursue this, they improve their lot and lives.
So to reiterate: from a scientific perspective, this is not a practical problem that doctors would face under true captialism, and morally speaking (which, in Rand's view, is exactly equivalent to the practical), there is nothing that can exist that is better than capitalism.
How do you fund the state, which is required for the provision of certain public goods like the common defense and that in most libertarian schemes enforces contracts?
Also, modern societies cede a monopoly on the legitimate use of force outside of self-defense to the state, which prevents revenge cycles (vendetta) and allows trust beyond families and clans.
The US and Japan are high trust societies and that makes a big difference in being able to do business (contract enforcement is a last and generally unsatisfactory resort) and all sorts of things we think as good. I think among other things that needs a state of more than minimal strength.
The government should sell optional contract insurance, which gives the contractual parties the right to go to court (or perhaps expedited enforcement in court) if the contract is not met. The rate should be capped at some small percentage of the contract's value - say 1%.
But the exact method doesn't really matter; in a society that such as the one I am speaking of, surely there will be many who will see the obvious selfish gain in maintaining a limited government that it totally dedicated to the defense of their individual rights.
And the public choice theory says it's not possible: http://en.wikipedia.org/wiki/Public_choice_theory