Last week, Anne Kornblut profiled White House counsel Robert Bauer for the Washington Post, in generally flattering terms:

For Bauer, whose expertise is elections law, health care may be among his easier assignments. He has inherited a vast national security portfolio that has become the core of the counsel’s work since the terrorist attacks of Sept. 11, 2001. His office addresses so many complex and unprecedented international questions — including the legality of capturing or killing terrorists abroad, intervening in cyberattacks, and holding suspects indefinitely — that people who work with Bauer said he now spends as much as half of his time on national security. It’s an abrupt departure for a man who just two years ago was challenging campaign finance regulations and monitoring Texas precincts for Obama.

His biggest burden: where the government should try Khalid Sheik Mohammed, the self-declared mastermind of the 9/11 attacks. Bauer started the job the month after Attorney General Eric H. Holder Jr. announced a civilian trial in New York — a brazen decision that has since been dropped. Now, Bauer is trying to think bigger and consider all Guantanamo detainees and suspected terrorists captured abroad in one proposal, rather than case by case. That “Grand Bargain” may include new legislation, which the White House had previously said it would not seek.

Kornblut doesn’t seem to see anything unusual about a White House counsel who rolls up his sleeves and gets involved in some hairy prosecutorial decisions. Nor does she seem to recognize much of a contrast with his predecessor—other than perhaps one of style.

Today, Huffington Post editor Dan Froomkin digs deeper into the issues that Bauer is facing and offers a more critical take on his game plan. Froomkin’s bottom line: with Greg Craig gone, expect that legal decisions will have far more political content. The dynamics are plain enough. Craig clearly was at cross purposes with chief-of-staff Rahm Emanuel on a number of legal issues, with the President’s commitment to close Guantánamo topping the list. Craig took the campaign pledge seriously and objected to the notion that legal policy questions surrounding the criminal justice system generally and decisions to prosecute individuals in particular could properly be part of the political give-and-take. Emanuel viewed them as a platform for bargaining with Republicans. Craig’s departure and Bauer’s arrival seems to have opened up greater latitude for Emanuel’s discussions with Lindsey Graham. Here’s how Froomkin sets the stage:

Holder decided in November that the trials should take place in federal court in New York City. But concerns about traffic and security eventually led New York lawmakers to oppose the move. And Republicans — who are still defending former president George W. Bush’s failed attempt to create an alternative legal system for terror suspects — piled on, accusing any Democrats who favor federal trials for the likes of KSM as evidence that they are soft on terror. Suddenly, administration officials were on their heels. And, rather than stick up for their attorney general, they started the process of undermining him.

White House Chief of Staff Rahm Emanuel, in particular, has long considered the issue a political loser, and is widely reported to be trying to strike a deal with Sen. Lindsay Graham, a South Carolina Republican, to make it go away: In return for the White House overruling Holder and sending the five most notorious suspects to military commissions, Graham would deliver GOP support for the rest of the White House’s plan to close Gitmo. Emanuel is apparently even wooing Rep. Peter King (R-N.Y.), the bombastic ranking member of the House Homeland Security Committee, who opposes closing Guantanamo and supports a ban on civilian trials of terror suspects. According to the Hill, Emanuel told King that he was “on his side”, although King wasn’t exactly sure what Emanuel was talking about.

For the Beltway punditry, of course, this was all evidence of Emanuel’s instinct for the good political play. But Froomkin sees another side to the story:

Decisions about whom the government should prosecute — and how — are precisely the kind that shouldn’t be made on political grounds. The American justice system is supposed to transcend partisanship, and be beyond the realm of political horsetrading. There are limits to how much the White House should do when it comes to interfering with the Justice Department — limits that, unfortunately, every modern president seems to push. And with Bauer serving in Craig’s place, the pushback is lacking.

It’s still early to be making any judgments about Bob Bauer’s performance as the president’s lawyer. But it’s definitely time to be concerned. The firewall between the criminal justice system and the White House was dismantled and hauled out during the years when Karl Rove sat at the president’s right. Today, there is every reason to fear that that change is being made permanent.