There shouldn't be a rogue timer at all. Once you go rogue you should stay rogue until you are either killed or leave. Just give bonus xp for every 60 seconds they stay rogue or something.
As far as I know. Once you murder someone you don't get cleared of charges because you stay hidden. You're wanted for murder for the rest of your life.
Also. If you continuously go rogue you should get rep as a rogue and eventually you're a rogue forever... Same goes with people that kill rogues. The more you kill, the more bonus you receive for killing them.
Make people pick a path.. Not just magically get cleared of being a jerk because you go afk for a while.