I feel the same way about the need for a pure defensive ship for use against the avatars and overlords. In my experience I usually start with Axes and then upgrade to dreadnaughts for defense. I have come to realize though that for defense of colonies, a good defense is not the only thing you want, due to how the combat system works in GalCiv. You also need a good attack rating to have an efficient defense becaue after the first round of attack, where your defensive value is versus the attack value of the offensive ship, the roles are then reversed in the second round, where your defending ship is now the attacker...thus a good attack value is integral in your defensive ship in order to efficiently counterattack.
Also, its not well stated anywhere but planetary defenses, start system defenses and omega defense system only affect your troop ratings in resisting invasion and have no effect on orbitting defensive ships. However, orbitting defensive ships do have a 100% bonus added to their attack value which is also not mentioned anywhere except in these forums. This does help substantially in defensive counterattacking.
And to chime in about the starbase issue, it is a good idea to build a military enhanced starbase in your border colony sectors. The offensive upgrades again help to boost the counterattack abilities of your defensive ships.
Finally, I do still think that there is a need for a later stage defense enhanced ship that is cheaper than avatars and overlords but can effectively defend against them. The whole counterattack issue is null and void if you can't make it past the first round of attack. Otherwise, its hard to win the game purely as a trade czar or a cultural icon and some military action is always required.