On the other side, Apple was found guilty of conspiring with publishers to make it absolutely impossible for other resellers to sell their books cheaper than Apple. If Apple had just demanded that they got the same or lower price on ebooks as other resellers, then they would have likely escaped litigation.
The situation is quite a bit more nuanced than that, and you've got your basic facts surrounding the case slightly wrong, since what you've stated Apple should have done is exactly what Apple did do. But, strangely, they also did what you said in your first sentence too. The illegal collusion and price fixing that's happened here revolves primarily around the interplay of two otherwise-perfectly-legal ideas: the agency model and most favored nation (MFN) clauses.
Agency Model: The agency model allows the publishers to set their own prices at the cost of giving the seller's a higher cut, whereas the wholesale model that is more common provides the publishers with a bigger cut at the cost of letting the sellers set the price. Given a perfect world, the wholesale model is more appealing to publishers, since they generally get a larger overall cut.
MFN Clause: An MFN clause is exactly the concept you described at the end of the quote I pulled above. They simply stipulate that they'll give you the same or better prices than they give anyone else. As you said, there's nothing wrong with that, in and of itself.
Background: Prior to Apple's arrival, Amazon had wholesale agreements with all of the publishers. The problem for the publishers, however, was that Amazon controlled over 90% of the eBooks market at the time. As you correctly pointed out, the fact that they had a monopoly wasn't actually an issue, since Amazon's interests (i.e. driving Kindle adoption and buy-in to their ecosystem) were better-served by keeping prices low, meaning that they were not using their monopoly in an anti-competitive manner. That said, they were using their monopsony in an anti-competitive manner, by forcing the publishers to sell their books at unreasonable prices while preserving their own margins, simply because the publishers had no one else they could sell to. In fact, there were several dramatic examples of Amazon using its monopsonistic bargaining position to strong-arm the publishers for better wholesale prices. Amazon was unwilling to discuss switching to an agency model, so the publishers were rather concerned that they may be forced to price themselves out of business.
With Apple—a big player— entering the market, Amazon was forced to negotiate terms that were more favorable to the publishers, namely, switching to an agency model. Such a change would naturally result in prices going up, even without any sort of illegal price fixing or collusion taking place, since the sellers are getting a larger cut with the agency model, which means that the publishers need to raise the prices to preserve their cut. Again, there's nothing illegal about that (in fact, it's what they're all doing now after what they were doing before was ruled illegal); it's simply a costlier way of doing business.
The Illegality: According to the judge, what was illegal in all of this was combining the agency model with the MFN clause. By combining the two, the MFN clause that says "you must give me the lowest price" in effect means "you'll raise the prices customers are paying at competing stores to match mine" (hence why both of your sentences that I quoted were what happened). Had they stuck with the wholesale model, the publishers could only have abided by the MFN clause by changing wholesale prices, so it would have still been up to Amazon and Apple to compete on price by deciding how much of a margin they'd (not) keep. Had they dropped the MFN clause, you'd have what the judge is forcing them to do now, since she's barred them from using MFN clauses with the agency model that the industry has now entirely switched to.
Moreover, court documents indicate that Apple and the publishers knew full well what they were doing and were indeed colluding in ensuring that prices went up in such a way that both the publishers and Apple would get what they wanted, with Amazon unwillingly being dragged along. That's why the judge is also forcing Apple to stagger its renegotiations with the publishers in six-month intervals, that way it's more difficult for them to collude with one another.
My Take: As for my opinion on all of it, I think that there's no one entirely innocent here. Apple and the publishers clearly engaged in illegal activity, and for that there should be consequences, though I think that the amount the judge has suggested in the original (DoJ) suit is unreasonable, since she's placing the burden for the entire increase in price on them, completely disregarding the fact that there were perfectly legal factors that also contributed to price increases during that time. Likewise, I'm wholly in favor of the class action suit against them, since consumers deserve to have a chance to collect what was taken from them illegally. That said, I also wish someone would take Amazon to task over their role in it prior to Apple's arrival. They had artificially pushed prices down through anticompetitive, strong-arm tactics, which is part of why the increase in price seemed so significant.
And as a closing thought, I hate to be put in a position where I'm defending the publishers. I feel filthy doing so, but I still think that the judge has been too harsh on them, even though they deserve to be punished.