Usually in Galactic Civilizations, a ship that is being upgraded can't do anything so if I have a constructor with constructor points that is upgrading to something else, the starbase should not be added in the "Update Starbase" queue. The constructor is updating so it cannot do anything.
I have used the following tactic to avoid constructor spam:
Using the designer I created two identical ship models (Med Cons 3XA and Med Cons 3XB) which is composed of 1 Medium Hull with 3 constructor modules.
I send the constructor "Med Cons 3XA" to a star base and use 2 of the 3 constructor points, then I upgrade it to a 'Med Cons 3XB' constructor. I repeat the process except this time I save 1 constructor module to keep the ship and upgrade to "Med Cons 3XA". This way, I don't have to keep sending constructors to that starbase. The only annoyance with this technique is that the upgrading constructor shows up in the "Upgrade Starbase" queue. It shouldn't as it's being upgraded so unavailable to construct anything. The current work around is to click on "Pass" but it is annoying to have to do this for every star base.
Thanks.