Why didn't Janeway use the invasive program that was developed by LaForge and Data in the TNG episode "I, Borg?" Nechayev ordered Picard to use it if the opportunity presented itself again in the future, so it's safe to assume that Starfleet didn't disapprove using it and stood by Nechayev's decision. You'd think there would be a standing order to use this program at the earliest possible convenience by any ship captain and its crew if Starfleet disagreed with Picard's stand that the program amounted to genocide. I doubt a matter of this magnitude would be left to a Starfleet Captain to use at their discretion...