IANAL either, but they're not being penalized for doing a bunch of legal activities, they're being penalized for the collusion. The penalty is a limitation in their ability to make contracts using the legal activities they used during the collusion so that it will be harder for them to collude again in the near future. This includes forcing Apple to stagger their contracts with the publishers.
There's nothing illegal in the way Amazon got it's monopsony by sometimes selling ebooks cheaper by accepting lower profit margins, providing an easy way to buy ebooks and install them on the ereader, and creating ereaders that could only decrypt DRMd ebooks sold by Amazon. In general, once a Kindle owner, always a Kindle owner thanks to publisher DRM. If the publishers wanted to make it harder for Amazon to keep their monopsony, they should have dropped DRM or changed their contracts to stipulate the ebook format so Amazon couldn't lock Kindle owners into Amazon's proprietary format. Just because the publishers were afraid that Amazon was going to use it's monopsony to keep prices lower (a la Wal-Mart) doesn't give them the right to engage in collusion to fix prices.