i think the use of the baseships was to even the odds against galactica, during the main attack the raiders could jump in and out at leisure as the colonial defences where shatterd with the CNP backdoor. So there was little risk of fighters intercepting, as well as and AA fire and flack.
Also the baseships where bussy with the inital nukeing of the colonys. So the raiders would of been used for lightning attacks simultainiously against colonial defences to throw them off.
Its hard to mount an effect counter attack if the enemys hitting you everywhere.
Galactica was pritty much a fully active battlestar so the raiders needed the base ships for support, otherwise they would get chewed up by galacticas flack and AA fire, with vipers cutting them down aswell.
in the great cylon turkey shoot episode where boomer infects the raider attack force with a virus there where no baseships preasant. Mainly because the cylons beleived that galactica would be imobilised by a planted cylon virus from when they networked there computers to compute the location of the missing fleet.
So the ship would of been unable to attack the fighters. with only the vipers left to contened with something like 300 cylon raiders and heavy raiders. The cylons probably beleived baseships would not be needed.
For all we know the cylons where still fighting colonial holdouts around locations in colonail space.
so there forces where stretched a bit thinner than we would think. I mean its silly to think that galactica would not be the only battlestar to not be affected by the CNP.
