People continue to think that the moral taxonomy helps you avoid slipping into the morality that is currently fashionable or politically correct because it employs scientific rationality. What they fail to see is that it doesn't really matter what kind of moral sensibilities you have - conservative or liberal - because you can justify either side of any reasonably difficult moral issue with the full backing of the taxonomic method. It really only works effectively when the combatants are two or more levels apart, as is the case with the oft-cited 'patients and germs' example, and then only under normal circumstances. If the doctor is starving, the most moral thing to do might be to let the patient die, then eat him.
You'll recall that when combatants are just one level apart, the lower level combatant prevails if you can justify to yourself that the higher level would jeopardize itself by defeating the lower level. This might be the tact an ecologist takes to justify saving rain forests, for example.
In another example, Platt Holden rationalized visiting his grandchildren (social) instead of posting to the forum (intellectual), on the mere basis that the social level was supporting the intellectual level - a much weaker justification for level reversal.
And then there's Struan Hellier's example of the morality of the American Civil War, which he details in his review of Lila on Amazon.com. Here you can mold the taxonomic method to your liking by taking advantage of level ambiguity, whereby a man is treated as a biological entity in one context and an intellectual in another.
So all these back doors to the taxonomic method really make it too flexible and unhelpful as a tool of ethics.
Essentially, people make moral decisions based on something close to Pirsig's method without being conscious of it. To his credit, Pirsig's accomplishment is that he discovered at least some of the underlying principles that already guide peoples' moral decisions. However, he failed to see it as a discovery, and thought instead that it was a new high-powered moral tool of his creation. And in his enthusiasm, he does a disservice to his readers by only showing how the method responds to fairly easy moral issues, and then implies that the reason the method is so effective is because it is objective and scientific. If you believe this (and this is where the real danger lies), you might be seduced into quick moral judgements without the thoughtful consideration you formerly applied to moral issues, all because you are smug about the ability of the framework.
I would certainly be wary of a dial-a-level mentality for the purpose of moral, economic, and political decision making, especially if it's done by a self-proclaimed intellectual who defines the levels to his own liking. The MOQ's intellectual elitism is reminiscent of Social Darwinism and eugenics in that they are all vulgarized extensions of biological evolution. Most people have concluded that such extensions are bad ideas, and like the MOQ's moral taxonomy, most early adherents were falsely led to believe that these ideas had scientific backing. Bosh.
Why he thinks the taxonomic method is objective or scientific I can't say. Certainly it was not arrived at by scientific means. He did not apply the scientific method here. Further, the taxonomic method does not resemble the scientific method, otherwise you'd do experiments to reach moral judgements. The only thing I can think of is that the taxonomic method has an algorithmic, cook-book quality to it that faintly resembles something that science might produce.