Well...I just don't think the Gatling would care as much about protecting the humans as it would think about killing the AI.
Then you are saying that this possibility of the Gattlings unintentionally putting you in a very bad situation is an acceptable part of the risk? Considering that there is at most only one Dyson sphere per game, and you have to explicitly choose to free it, that doesn't seem unreasonable. But maybe a warning in a tool-tip (either for the minor faction description or on the Dyson sphere itself) about how they can start freeing stuff haphazardly (by killing guard posts) may be in order.
Or maybe just not allow Dyson gattlings to target guard posts. That seems like a simple solution. There are already provisions in place to stop the AI from freeing stuff due to minor faction intervention, so long as what a ship is guarding stays alive. If they cannot target guard posts, then Dyson gattlings can wander throughout the galaxy all they want and you don't have to worry about them accidentally sending stuff your way.
Human resistance ships need to either get this same targeting restriction or be disallowed from
entering enemy planets without a human player doing so first (if they
spawned on an enemy planet, you were attacking it anyways, so no harm there). Human resistance ships spawn too frequently on factors not entirely under your control for the risk of unintentional freeing to be introduced.
Again, less of a deal with zombies; you were warned about their mindless over-aggressive behavior.