Come to think of it, why didn't they ever back up Data?
Yeah, they also must have made about ten thousand copies of the bootup state of the EMH's program. No way they programmed 10,000 EMHs individually.
It is pretty weird that after refusing to give Starfleet tech to the Kazon they give it away like candy in several instances later in the season. Besides that I don't see any issues with the Hirogen thing though. It did end up saving lives, it made fewer Hirogen hunt actual living beings. They just didn't know the Hirogen would end up turning their holograms sentient.