I think that Partridge was killed because he stumbled upon a plot between Bertram, Reede Smith, and McAllister. McAllister killed Partridge. He didn't know Lisbon was tracing their phones. I think she surprised him when she showed up and he tasered her before she could identify him. He drew the smiley face on her to make it look like Red John murdered Partridge. He quickly left the scene when the pigeons started flying. In the most recent episode, we see he doesn't like birds, yet admits he likes to hunt "anything with a face" and doesn't mind the blood. How Red John knew she was there and was in danger I don't know.
