the cycle is meant to establish proper bacterial populations. these organisms are non-photosynthetic, so the lights will have practically no effect on them. however, any photosynthetic organisms that you had in the live rock will die off, negating many of the benefits of buying good live rock, so, imo, lights are a plus.
not to mention that many types of flora can be good indicators of where you are in the cycle, based on the growth patterns...