The Alliance was aware that fighter sheilds did not work in subspace, but until the nudge in thinking from the Ancients records, no-one apparently associated the phenomenon with the Lucifer. The Allies were also aware that vessels could be tracked in subspace, but again either did not put the ideas together or simply did not have the know how to make it reality. That is the major assistance that the Ancients really gave.
The real issue I can see of dealing with a Lucifer class capitol ship within the story as it exists is the very narrow focus of the Allies' attempts to deal with the thing.
No one tried ramming it with an Orion or a Typhon or three for example. I'm fairly certain that much metal in motion would cause the Shivans some headaches. Heck, you could hedge your bets by loading up the sacrificial ships with some really nasty antimatter bombs. Fill the forward sections with sand or junk or cement or whatever so it could take a hit or two from the beams and fighter escort the hell out of them until impact. Lucifer was not the most spry lass at the ball, so ramming should be feasable.
Just some thoughts. Seemed to me like the GTA and PVN were trying to think in terms of equalling the Lucifer, rather than playing dirty.
In the entire conflict, the Shivans only showed a slight tech edge in real terms. The major battles they won were mostly due to the presence of their unkillable gunboat.
It seems to me that the Lucifer was probably more of a one-off ride to the Shivans: it was the only one of their vessels armed with beam weaponry at the time of the Great War. At that it carried only two of them. Unlike their other ships it required five dedicated reactors to power its shields and guns, unlike the other or even the later ships in the Shivan Fleet.
I'm thinking that maybe when the Lucifer was broken the baddies decided they needed a new kind of hammer - thus the Ravana and other beam armed ships.
The Sathanas has me thinking more on the lines of Shivan colony transports than as being intended for fleet action. Yup, they're huge and massively armed, but rather unweildy as a dedicated military unit. They were rarely committed to battle, and then usually to fufill a set goal. The story does show them jumping out as Capella novas, while the smaller units are engaged in tying up the GTVA forces to prevent interference. We have no way of even knowing if this was the same branch of Shivans that participated in the Great War: this group came from beyond Gamma Draconis; the earlier invasion came presumably through Ross 128. Just to throw a bit more on the thought fires, it could also explain no Lucifer class ship(s), and the difference in choice of armanents.