I believe that Van Pelt is definatley connected to red john. There is a picture on the website screenshot.com/the mentalist season 5, which shows all the main 5 characters on it. Jane is sat on a couch flanked by cho and lisbon which shows they are his closest allies. rigsby and van pelt are stood up. rigsby is facing the 3 on the couch where as van pelt has her back to them looking at them in a mirror. I think this is a message from the writers to say that van pelt is not all she makes out to be.
I agree with many theories that van pelt has lost a family member due to Janes con artist scams and therefore is working with red john to destroy and hurt Jane.
I think she used O'loughlin and then was given orders to kill him by red john. O'loughlin was sent to the safe house by red john to be killed by van pelt.