We're so close to the end that I think this is the last attempt at misdirection by the writers. Billy helped clean up John's mess and John was most likely the killer. There are a few surprises they can still throw at us but they would be too over the top.
The biggest question and the elephant in the room for Episode 6 is that no one has asked "Why would Billy kill her"? I mean, its pretty straight forward, right? The Dad didn't ask John, John didn't ask his Dad. John's wife told Mare that Billy was the killer because he incestuously impregnated his cousin's daughter. Yeah, and? He decided to wait a few years to kill her? Why?
So, the obvious answer (outside of what the writer's are trying to have us believe) is that John impregnated Erin; John & Billy killed Erin & has now manipulated Billy in to taking the wrap for him. We have all the clues we need to come to this conclusion: John is promiscuous, John (According to Billy) doesn't take responsibility for the messes he makes, etc..