Personally, i like the idea of there being other military ships, for jobs that dont require the size/power of a battlestar.
Also, in a mdoern naval fleet, you obviously have the Carrier, which can deffend its self to a certain extent, but they do have Escrots such as Submarines, Frigates and Destoryers. In the Royal Navy, Destroyers are Anti-Air (so in space, they would be responceible for defence from fighters and missiles, working with a battlestars FLAK, that would make an almost impenitrable defence), Frigates are Anti Submarine, so not required in space, Submarines are used to attack surface ships, so in space they would be used to attack a target, presumably while being covered by a destroyers flak or missiles for defence.
After that, theres theres Patrol ships, but Raptors fit that role, as they also fit the Transport, EWAR and Bomber roles. While Vipers fill th role as a fighter.
I just dont see the point in havign a fleet full of battlestar, which probally cost alot to build/maintain, when you can have smaller faster ships capable of doing roles