With wholesale the publishers are not involved in the consumer's price: the publisher sells to Amazon for a fixed price and then Amazon sells it at the end consumer at whatever price it wants. Amazon selling an ebook at loss means that Amazon loses money, but the publisher's cut for that sale is not affected at all.
This is where you're wrong. If the publisher set the retail price at $15, they're expecting to make $10.50 per copy after Amazon takes it cut. But if Amazon discounts the price to $10, the publisher gets $7 after Amazon takes it cut. Amazon wasn't compensating the publisher for the missing $3.50.
Under the old rules, Amazon was allowed to build a monopoly by forcing the publisher pay for the privilege. Why? Because Amazon is "the world's largest market," which is shorthand for, "bend over and say, 'May I have another, sir?!'"
Apple comes along with a proposal to change the rule. The publishers jump at the opportunity to stop subsidizing the Amazon monopoly. More competition is a GOOD THING. Even if that meant in the short term that buyers would pay more for ebooks.
Competition from indie ebook publishers like myself will eventually force the traditional publishers to stop protecting their dead tree monopoly and discount their ebooks to $3 each. Buyers will win out in the end.