If defending ships still run up and die by themselves(haven't had a starbase attacked yet) then I don't see a problem with starbase strength eclipsing early fleet strength, because you can't actually bolster their defense. Clearly, all is not balanced, but nothing wrong with a static military installation wiping the floor with a small fleet.
They were tissue paper, it was embarrassing how easy it was to drop a static object, it added a great deal to the mediocrity of the game by having to constantly replace the stupid things every time some random ship bothered to remove one even though you spent 20 constructor modules in an attempt to make it not be a free kill. They could probably use an initial defense addition or two and start out with substantially less stats so you actually have to spend some money to make them invincible, but it's not like they're actually invincible.
Throw a flagship and an admiral in the mix and you can knock one down pretty easy with early weapons and defenses and that first logistics upgrade.