Not so much a theory on who Red John is, but more of a theory on the sequence of events on the next episode...

Patrick is approached by Bertram in the church and is about to kill him when he begs for Mercy. Right before Patrick shoots him, he admits that he is not RJ but he knows where he is. He tricks Patrick and takes off running explaining why Patrick shoots at him in the church.

Next, Patrick spots someone watching him at the cemetary and a foot chase takes place. It is McAllister and during this chase he crashes through the sliding glass door. Not sure if they catch him or he gets away.

Finally, Patrick gets a call from RJ wanting to meet him in the park. This is it, the moment of truth. Bertram is still on the run, but not RJ. The team pull their guns on the FBI agent to give Patrick the chance to face RJ alone in the park. I personally don't think McAllister or Bertram is RJ, but at this point everything is possible. I expect to see Partridge, but this scenerio leaves it open for any of the 7 suspects to step out and face Patrick in their final showdown.