RJ is not dead,
When Kimbal goes to check on the dead body of partridge you don't see the face.
But the tattoo is cut of his arm.
The only reason is because the body is replaced with another body.
When Jane tells mcallister how he figured out how he wasn't killed in the explosion, the name of partridge came to mention.
He had the ability to replace dna or put other bodies on the crimescene.
And that's the only reason the tattoo is cut out of the arm, because there never was a tattoo.... Because it's another man.
Last but not least, Jane knows about this. If RJ was mcallister, he wouldn't have come to the chapel. Jane had no other chose then to kill mcallister so RJ could take his time hunting him. And when RJ is close, jane will be waiting for him to strike the final blow.
