I've been sitting on this story for a few hours, waiting for the Kennedy Center to get back to me with a comment. No comment yet, but if they ever chime in with something, I'll update.
Update: Finally heard back from the Kennedy Center folks. Here is the official statement from their press office regarding Beck's appearance and comments from this morning:
The Kennedy Center was informed that as part of its event on August 27, Mercury Radio Arts desired to lead the audience in prayer. After checking with our legal counsel, we found that this did not contradict the rental agreement for the event.