Part of the deal with Apple, and I suspect this is what caused the action of the DOJ, was that the publishers were required to prohibit retailers from discounting their E-book offerings to customers. So yes, they were colluding to fix prices, just not by a certain dollar amount.
No, that is an incorrect interpretation of the "Most Favoured Nation" clause. The clause stipulated that the publishers, who set the prices in the iBook Store had to 'match' the lowest price offered at other ebook stores. The publishers were not prevented from discounting or putting books on sale and Apple, at no time, had any influence on the price of books on their own store or anyone else's. There is a big difference!
What Apple was trying to prevent was having the book publishers put Apple's iBook Store at a disadvantage price wise as compared to their competitors since they were not in control of the book pricing. Get that, Apple was not in control of the price of the ebooks!
I will state this now, Apple will come out of this unscathed. The DoJ has no case against them according to statements released so far. There is nothing illegal in Apple's contract with the publishers including the MFN clause. It is no different than the deal they have regarding App sales except for possibly the MFN clause.
If the publishers used their deal with Apple to pressure Amazon into a new deal that isn't illegal either that is just contract negotiation.
The only thing the DoJ has is the collusion allegation and, again according to statements released so far, they haven't produced any evidence that the two hold out publishers and Apple colluded amongst themselves or with the other three publishers in this contract arrangement. They state that they have evidence of meetings amongst the publishers but two of them deny involvement as does Apple. It may be that the other three publishers who settled were the only ones involved in those meetings and that is why they settled.
As a matter of fact one of the pieces of evidence produced by the DoJ contradicts the collusion argument. According to the DoJ Penguin Books asked for 'assurances from Apple' that the other publishers were going to also join in to the Agency Pricing model. If there was collusion then Penguin Books would not have needed Apple's assurance (and there is no evidence Apple gave any such assurance), they would have known from their own meetings with the other publishers that they were going to join with Apple in the Agency Pricing arrangement.
Notice that Penguin Books is also one of the hold outs in a settlement with the DoJ.