The main reason that the agreement is deemed illegal here is that they were made with a specific intent to manipulate the market at large and because they are deemed to have kind of market power, being a cartel of large employers. Also, the nature of the agreement is far too broad and the companies involved is far too numerous for them to argue in good faith that their intent was much more narrow.
I completely agree that they overstepped and should be held liable, but some of the outrage seems misguided. The HR executive involved, for instance, may or may not be in position to know that the policy is part of an illegal scheme and the fired employee certainly was not. Also, unless you're one of the star programmers who were highly in demand, it's quite unlikely that your salary was all that depressed over this. If anything, the impact may have been slightly positive for average employees - at a lot of places, superstars aren't necessarily substitutes for average employees, but rather complements and lowering prices of superstars can boost rather than depress wages of average employees:
http://www.joelonsoftware.com/articles/StrategyLetterV.html
On the whole, this is kind of the replay of the Microsoft anti-trust trials. Bundling web browsers with operating systems is not illegal - the illegal part was the context in which such action occurred. It was seen as an abuse of market power. Sports leagues openly collude on this kind of stuff without most people caring at all or pointing fingers at those involved. Government can have strong interest in such matters in the interest of encouraging a healthier market - though political and career motivations of lawyers/prosecutors involved also play a large part - but to seeing this as a clear morality play is not wise.
Edit: actually this covers the legal issues better:
http://www.mondaq.com/unitedstates/x/258600/Antitrust+Compet...
Assuming the article is correct, having a general agreement without any specific, legitimate purpose is illegal, but on a limited basic it can be legal. Still it seems far-fetched to assume that the HR executive in question had to know that such an illegal agreement existed, because for all he knows, a much more limited, legal contract could have existed due to their partnership and Google may have had a broader policy to ensure easy compliance. We now know that that's not the case, but I don't know why we can assume that the HR executive necessarily was aware of all this.