The article notes that

The announcement is aimed at making sure that no court or party to a lawsuit can cite the Bush administration policy as the government's official view in any pending cases.

In the speeches, Ms. Varney is expected to explicitly warn judges and litigants in antitrust lawsuits not involving the government to ignore the Bush administration's policies, which were formally outlined in a report by the Justice Department last year. The report applied legal standards that made it difficult to bring new cases involving monopoly and predatory practices.

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Antitrust policy is set by Washington in two ways: by the interpretation of laws announced by the Justice Department and the Federal Trade Commission through guidelines for the courts and private litigants, and by the enforcement cases that those agencies decide to bring. The government's guidelines are often cited by lawyers and given considerable weight by judges in antitrust cases, including those lawsuits that the government does not participate in.

This "warning" to not use the Bushco guidelines is of a piece with the Obama OLC rejecting the torture and interrogation memoranda put out by the Bush OLC in the first days of the Obama Administration and warning people not to rely on them any more.  The DoJ's antitrust guidelines are pretty critical information as to what the government says constitutes a violation of the antitrust laws and what does not.

As to whether a Bushco appointed judge will, or will not, follow the change in guidelines, I would expect them to find a way to implement their ideology - the Bushco ideology.  Antitrust enforcement and theory is (and long has been) one of the drier deserts in the legal world, but it is nonetheless perhaps one of the most critical.  That lack of consideration for it stems from a fundamental misunderstanding of where antitrust lies in the structure of checks and balances.  

One can have all the rights one could enumerate (plus all the unenumerated ones) but if one cannot get a foothold into a market to make a business and keep it going - because some big company has a monopolistic control over that market - those rights aren't worth much because you cannot eat rights and you cannot spend them.  If that monopolist then decides to shove a few crumbs from its table to pliant Congresscritters, they can then get all the laws they want written to their order and those rights are worth even less.  Let's not forget that prior to the 2006 election, lobbyists were writing entire bills for Congress and the Repugs were dutifully passing them into law and Bush signing them.

The antitrust guidelines give potential plaintiffs - the little guy - another, critical arrow in their quiver of antitrust enforcement:  The ability to argue that the government recognizes practices "A", "B" and "C" as violative of Sherman 2, and that the monopolist they are suing is committing "A", "B" and "C".

Not for nothing, the Repugs have devoted decades to vitiating the antitrust laws.   Some of their leading lights came up as antitrust specialists;  Bork comes to mind instantly, and Posner/Easterbrook and the whole Law and Economics crowd follow closely behind.  This should not be surprising, since the wealthy and powerful are the people usually either violating or looking for a way around the antitrust laws.  You want to make scads of money as a lawyer?  Go into antitrust defense.

And, for those who want to mock Randian theory, you should go read what she had to say about antitrust, both in her novels and her "philosophic" writings.  Most of what passes for antitrust theory - from the banker perspective - today could have been lifted straight from her books.  This is not entirely surprising, considering Greenspan was one of her students.