Very well put. A simple and effective start to this problem of thier starbase would be just to have the anti-structure already equipted. And maybe a reduced build time in an enemy well. Sounds like a start to me.
A variation might be to keep the build time roughly the same, but allow it to be started while in the phase jump, LOL. Would add some tactical decisions, and would allow for not only building the SB quicker, but also having some hit points accumulated on it when it arrives. Just creative brainstorming, ha.
I am just having this imagine in my mind: a marauder at lvl 6, a phase stabeliser, several migrators flying to the planet concerned, enough money to spare .... omfg the enemy is attacking with a fleet of starbases 
not a bad idea though, but I don't think it would help all that much. may some sort of stock anti-structure attack that can be upgraded later would help. dunno.
I mean maybe it's good to nail it down again what the problem is:
1) the vasari have something against enemy starbases, which is their own starbase.
2) in order for it to be effective, you have to get it there, construct it and give it at least one weapons upgrade.
3) if the enemy planet is halfway protected, instead of the weapons upgrade, you may have to go for a structural one first, in order to ensure it survives long enough.
4) that means by the time you have done all this, you have spent a lot of resources and time. time the enemy has had to react.
5) you spent all those resources and you cannot assault another planet with it. granted, you have strong defensive installation now, but a tec or advnet player just takes his investment in ogrovs or adjudicators at attacks the next world. though that would not such a big point necessarily, if the resource point was smaller. after all, you are free to move more of your fleet on, with a nice defense in place. the other races either have to leave forces behind, spend resources on defense, or risk an attack.
anyone agree or disagree with those considerations? then it might help in finding a solution.