Specifically, I'm curious why wouldn't you want your representative (your publisher) to have the power to achieve the best possible outcome for you, the author. Disregarding the specifics of this case, why would you trust Amazon to set your books' prices, seeing as how they're trying to subsidize a platform, and they're in the volume business?
Thought experiment: As a developer, would you support a decision from Apple to set a price ceiling of $0.99 for applications in the App Store?
I haven't really seen a convincing argument from Amazon's supporters why they feel Amazon should be able to set prices to goods they don't produce. That is, apart from the fact that these folks would like cheaper books--and that misses the point of what's at stake here. Even if you agree with Amazon on their current pricing model, it seems like an arbitrary and likely momentary alignment of opinion.
If MacMillan's ebook price system doesn't benefit them and their authors, they'll almost certainly adjust it. They're a profit-seeking entity.
As a side note, this whole episode reminds me of Walmart squeezing down the price of pickles by sheer monopsonistic purchasing power.