Turning the pickup round will be virtually switching the wires (I think) and if you don't switch the wires, it will be basically the same pickup, maybe a bit twangier, but hardly noticeable. It's pointless really :/ I have a HH setup with the Ibanez 5-way wiring and I had to have the Neck Pickup with reverse polarity. I'm not sure how it would work if it wasn't though, but I know for the 5-way, having the neck pickup's polarity reversed is pretty important.
Maybe send Tim an email an see if he can do something for you. Where did you get the pickup from btw?
Also maybe get a 3 way switch? You can get them to replace 5-way switches.