Exactly.
I don't know for what they were looking for in that nebula anyway, they found another Knossos and a lot of Shivans on the other side, so they should acknownledge that they are not welcome in this system, pack and leave. By the time of SOC mission it might have been too late for closing the node to nebula, but they could have cut Gamma Draconis, as it was useless. The only gain they had from the nebula was a possiblity of producing Prom S, but with NTF insurgency over they would not need it.
Well, there were a few things.
1. the most important of all, the first Knossos. Petrarch says in the command briefing of the Battle of the Wilderness:
Allied scientists studying the portal remain optimistic about the potential for this technology. In five to ten years, we might be able to restore contact with Earth or create new jump nodes to unexplored regions of the galaxy. For this reason, the portal must remain open for as long as possible.
Command has issued a standing order to destroy the device should a full-scale invasion be imminent.
It was imperative to gather as much available information as possible about the gate, that's why they have kept it active until the last possible moment. Obviously, this point becomes moot after the destruction of the Knossos, however here comes the second argument...
2. In the same briefing, we can read:
The Shivan fleet appears to be smaller than the armada we defeated three decades ago, and our improved technology gives us a tactical advantage.
The GTVA believed that they could handle the threat. They actually did quite well, if you don't count the first Ravana, and managed to succeed in most engagements against the Shivans. They even managed to develop a strategy against an enemy Sathanas and defeat it. I wouldn't be surprised if the GTVA considered the Sathanas to be kind of a new Lucifer - they never expected that the Shivans could have an entire armada of them.
3. Aken Bosch. While the NTF Rebellion was basically over after Bosch's escape, somebody had to be punished for all the war crimes. In order to improve morale across the GTVA space and help stabilise the relationship with the Vasudans, they needed to capture him and his lieutenants and put them on trail.
Nevertheless, I still don't know why they haven't closed of Gamma Draconis the moment multiple juggernauts were discovered. The only explanation that comes to my mind is that the meson-armed Orions weren't ready until Shivans had already reached Capella.
