Ran through the Sphere of Influnence several times and thanks for fun adventure and access to new toys.
One question after defeating the elachi and the NPCs have a discussion about what to do with the gate. The Enterprise contacts Shon and mentions "an Omega" and that the computers and engines are offline (or something close to that).
So what is "an Omega" that is being referred to in the cutscene?
In the Voyager episode, after the shockwave from the destabilized particles hits Voyager, nothing is triggered. When they scan for the source of the shockwave, however, the directive kicks in and locks out the ship.
In the new mission here, none of the federation ships that arrive are locked down immediately. After the battle, they scan the gate and still nothing. It's only when the Enterprise actively tries to scan what's on the other side of the gateway do they trigger the directive and the lockdown.
It should only pose an issue facing a ship powered by Omega, in which situation shooting at it indiscriminately is liable to bring about the disaster the directive is meant to prevent.