In the next few months Obama is going to have to deal with two awful wars, a shitty economy and the disaster that is the automotive industry. To do so, he's going to need co-operation from both the left and right wing.
Yeah, Warren sucks, but he's not going to be in any position of policy. He's simply going to say some harmless words. Which, may give Obama some good will.
I'd prefer there be no prayer at all - but I'm also glad that Obama's first week in office won't be distracted by a week of news articles about there not being a prayer.