Please buy books, but not from Amazon if you can

Why is the US Justice Department taking on Apple in the war over the prices of e-books? Is it because the company has embraced the agency model which allows publishers to set prices while Apple keeps a percentage of the retail price? Forgive my ignorance but what is wrong with this model?
And why is there a perception that the wholesale model adopted by Amazon is better for the book industry yet Amazon gets to keep 65 per cent of a book's cover price while the author and publisher share the remaining 35 per cent? Is this fair to the writers and publishers? And where does that leave the two when they have to sell their books through an intermediary?
I am asking this because from where I sit, I am of the view that the Apple model is the lesser evil. Apple gets to keep 30 per cent from each book sold, which is the standard for booksellers even here in Kenya. The writer, publisher and intermediary can agree on how to share the rest. What's more, the likelihood of books being fairly priced is increased because all those involved in the chain can find comfortable margins that they can work with without fleecing readers, which means that even readers benefit and, therefore, have a reason to return for future purchases if they get value for money.
But if my briefing is correct, and I have no reason to believe it is not, if Amazon catches you selling your book at a lower price, say on e-bay for instance, it will withdraw it from its stock. I may be from Africa but is this the done thing in a free market economy? The impression I take away from this is that Amazon, with all due respect to its accomplishments and contribution to literature, is acting as a policeman. And now look what the Justice Department has gone and done.
True, all the players are still trying to define the rules of the game going forward but from the look of things, the referee appears to have worn one of the team's uniforms and I am not making this claim with any prejudice. In Kenya, we say we need a level playing field.
As a writer I would be glad if my books were available at Amazon. That would be a wow moment for me. But then again, if they were to be available in other outlets, say Kobo or B&N for the same price, I would need a great deal of persuasion to refrain from telling my readers: "Yes, please, you can buy my books online but not from Amazon if you can help it."
Can someone please tell me my fears are misplaced and that this is not what it looks like?