Exactly. Think of a Knossos as akin to an engineering team constantly shoring up the levees along the banks of a river to prevent them from breaking. Provided the engineers aren't a bunch of lazy bums, they can presumably fortify the levees faster than the river can erode them away. Now obviously, if the engineers packed up and left for good, the river would eventually undermine and destroy the levees, but provided they did their job well enough, it might take decades for that to happen. In the same way, the operation of the Knossos for the comparatively-short time during the events of FS2 was enough to stabilize it even after the Knossos's destruction, and maybe even for good.
Incidentally, I feel like that aspect of the Knossos ties in nicely with the "Lucifer fleet as cut-off remnants" theory. Based on the Ancient monologues, one would think that the Ancients shut down the Knossos in the face of the overwhelming Shivan advance, which ultimately proved futile in stopping the Lucifer. But by the time the Shivans completely finished off the Ancients and returned to the Knossos, perhaps it had been inactive for long enough to make the node impassable once again, trapping the Lucifer fleet on "our" side.