Wow so you did think this through very, very thoroughly. And I like the idea that the Ancients put up a fight. They conquered thousands of species, the Shivans couldn't put out the light that fast. 
*Shrug*
Based on the FS1 cutscenes and Volition's own statements about Ancient technology it seems that they did not defeat Shivan shielding until their homeworld was destroyed.
The Shivans likely blitzkreiged straight through their major systems, tearing their ships apart while "not dying," and crushed the Ancients rather swiftly. Their species was most likely reduced to a non-viable population by the time they had the means to fight back, not that it wouldn't make an interesting story about the surviving armada knowing it's doomed tracking and fighting the Shivans in subspace when all of their worlds were gone.
However it does seem to be a common theme in fanon to have the Ancients put up a good fight.
i always figured the ancients put up a good long fight (though not one long enough to seed life on our worlds, not to say that this couldnt have been the case earlyer in the ancients history). the ancients held a much bigger empire than the gtva. such an empire wouldnt have been conquered overnight. it probibly went on for a number of years. the lucifer was aparently built just for the final attack of the main systems of the ancients. im sure they had to face waves of sathani (perhaps even a dante or two
). perhaps in the fight the ancients crippled a great many jump nodes (by either porthole shutdown or just plane mesoning) to slow the shivan advance. in the process they probibly isolated the sathanas fleet as well as the lucifer fleet in an attempt to confuse the enemy.
the lack of beam cannons on the lucifer fleet? perhaps the ancients sent bombers and interceptors to cripple this final assault force. knocking out its beam weapons. while at the same time closing off themselves from their shivan foes. it the final hours of the ancients, they most likely would be thinking more of their survival than the successful outcome of the war. they would be running in battlestar galactica fashion, trying to cripple their few remaining persuers who have been sealed off from their larger fleets.
this leads them to what will be gtva space. we know gtva space is pretty much cut off from what, under the same rules of subspace, should be a galactic subspace network. the ancients did this on their final escape, lucifer fleet right on their tail. they sealed nodes, they sent ships to cripple the support fleet, however they were a little late to figure out how to kill the shields. and so they get wiped out, leaving the lucifer fleet stuck in our little area of space. probibly having gone into hibernation after a thorough search for a way home. they probibly detected the beginnings of intelegent life on vasuda and on earth, and probibly decided to wait until theese spiecies reached stellar maturity, at which point they would start killing eachother and possible figure out how to activate that infernal knossos.
