The Shivans didn't need the Knossos to travel to the Ancients systems, remember that the Shivans can travel through nodes the GTVA and possibley the Ancients, cannot, in Ross 128, Ikeya and Antares.
or maybe the travel is much lager without the gama dragonis knossos.
the gate was a shortcut, and without the gate, the travel is many years long.
we doesnt know where the gate end, in which part of the galaxy and where the next system is in our galaxy behind the nebular.
maybe this are over 100 or 1000 lightyears and you have to travel thourgh many system, if you want to go to this place without the knossos.
i mean the cutsequencen in Freespace, only say that the ancients retrieve to thier homeworld, and that than came the destoryer.
there was no directly allegation of time, between the retrieve and the arrival of the shivans.
maybe there that think, now we are save over 100 years but then came there nightmare back.
maybe thats the reason why they think the gods of the univeres are irate.