If it were just pandering, it would bug me. I don't think it is for two reasons:
1. Apparently Obama and Warren are friends, or at least acquaintances, and Obama refers to the guy in one of his books in friendly manner; and
2. I think Obama really does want to try to pull together, to the extent it is possible, people who disagree with him on issues. One way to do that is to be respectful about differing views. And one way to do that is to bring a guy like Warren in to do something like give a prayer. It's not substantive policy, but it's at least a tacit acknowledgment of a different viewpoint and a way to show respect for the differing views.
Unlike, for example, this site, I don't see any reason that the vast majority of liberals, conservatives, libertarians, socialists, etc. can't be respectful of one another's viewpoints even while opposing them as policy.