McAllister should have killed everyone (including Patrick) with the bomb except Bertram.  Then his plan of everyone thinking Bertram was Red John would have worked better.  Patrick had no idea about the bomb plan, he was just lucky McAllister saved his life (for the THIRD TIME I might add).  Bertram would have no idea that McAllister did it because he didn't know he was Red John.  Plus he would think sheriff was dead because of the fake body.  Bertram's best defense would be "I didn't do it, Red John must have planted a bomb."  But who would believe that story since he would be the sole survivor.  Bottom line, for a serial killer, I find it funny that Red John spared 3 (Jane, Smith, Bertram) and killed 2 (Haffner, Stiles) that night.  He should have just killed everyone or left Bertram alive to frame him as RJ.