At first I was dissapointed about the great Stiles dying in such an unhonorable way, but after thinking about it for a while I concluded he may have sacrifised himself.
Let's overlook what might have happened in the landhouse: Jane lines up the three Tigers, ready for a long interrogation/execution. Meanwhile Haffner is using Jane's focus on them at his advantage and tries to escape because one of the Tigers might know he's the real Red John. If he is, he has been there before and knows a way out of the house by the back.
Jane has a fast reflex, turns around and shoots him. He hit him, but not lethal, maybe he shooted off a finger or something (DNA 'evidence' after the cleanup).
Jane goes after him. Bertram goes after Jane to disarm and kill him (in the spirit of the Tigers). So they both are found in de next room after the explosion. Smith is reaching for his gun on the ground.
Meanwhile McAllister sees that Stiles is picking up a bomb (that might have been hidden in his shoe, what would explain the bare foot). He tries to stop him but it's too late, the bomb goes off and Stiles & McAllister are blown up. Smith was just far enough to survive, as were Jane and Bertram, who were struggling for the shotgun.
Stiles was the one that went to the army for a small but effective explosive. He knew Haffner, a lifetime protegee of him, very well, and probably knew he was Red John. Since he was allready a dying man, he debated the events with Haffner in advance and told him to run if possible, and that he would do the rest (or Haffner asked him the other way around). So there's DNA from three men, while only two are dead.
Jane knows Haffner is Red John since he tried to escape (Haffner was allready eager to leave before the gunshot) but uses the 'fact' that he deceased in his advantage and sets up Bertram as the perfect distraction. By declaring on TV that Bertram is the serial killer named Red John, he's ending things as they begun: by offending Red John publicly. Jane knows he's too proud not to come after him now.
