OK, what could Apple and the publishers have done to stop Amazon other than what they did? How to break Amazon's power to destroy the profit in making books? And more importantly, let the publishers decide things like what they'll charge (which is what producers usually do get to decide)
You act like this is a huge gotcha question.
Antitrust is a civil wrong that can be brought by a third party. You don't need the DOJ to file an antitrust case. If Amazon was truly exercising monopoly power, the publishers could file a lawsuit against them claiming treble damages and attorney's fees, and push for a reasonable injunction.
What they don't get to do is exercise self-help.
It's like this: If someone fails to pay you money they owe you, the law doesn't allow you to break into their house and take their valuables. You have to take them to court and sue them.
Inconvenient, yes, but the rule of law so often is--and I feel no sympathy for large corporations who can't abide by it.
The reason no publisher has sued Amazon claiming monopolization is because Amazon does not actually have market power under the current definitions of "market" and "market power." Back in the day, it didn't account for much more than 10-20% of book sales. Ebook sales were higher, yes, but print book sales? Nope. In the US at least, without market power, any of the things that amount to attempted monopolization are considered just good competition, and therefore beneficial to the consumers.
Even today, Amazon accounts for about 40% of book sales overall--which is precisely the share of the marketplace that Penguin Random House holds.
This really isn't a case (however its been spun) about small publishers being unable to take on Amazon the behemoth. The publishers who participated in agency pricing, with the exception of MacMillan, controlled a share of book publishing proportional to the share of the book selling market that Amazon controlled.