Well, you made a mistake of throwing the starbase alone (it looks like it from your description).
I too feel that the disintegrator arrays seem to be more effective against units than structures, rather than the other way around.
As in - they hurt ships badly while not being anywhere near 4 bomber squads when used against structures.
However, it isn't all that bad. Has high hitpoints when upgraded (if you manage to upgrade it - Vas vs Vas is screwed), decent damage (for the price), can defend itself. Needs support, yeah, but it's not something that's gonna disappear in 3 seconds.
Good idea is having 5 overseers around. They REALLY increase the survivability on the SB. Assuming 3 casts of nanite armor per Overseer (they can do more, but let's assume they made a jump or two or something) it is 15 casts for 3750 extra health over 6 seconds. Very useful imo.