you could wire it so that the power from the stator energizes the relay. that way it would only light the lights if you had a charge. keep the lights wired to the battery.
nice thing about our bikes is we have kick starts and they aren't 600cc's so if the battery dies it's not THAT big of a deal. also a 100w stator is gonna charge the battery pretty quick.
I liked having the lights wired so they'd run even if the motor was off though, helps with a night time situation where you need to dismount, shut the motor off to talk and find your way type of thing. nice when your flash light is buried in the pack and yo ustill need light.