Can't you see the scenario? Red John will be back. That's how: 
Red John sent Agent Pike to Teresa Lisbon. When they became lovers, Patrick Jane got jealous. I mean, Red John urged Patrick Jane to declare his love to Lisbon... And now they became lovers.
Now it's Red John's turn. He will come back and kill Lisbon. This is a familiar case, right? Red John will take Patrick Jane's love for the second time.

Let's wait and see