I have a few ideas for this problem:
- There should have been more penalties for having a starbase on the territories of others. The owner of the area should be able to tax the starbase, both it's economy and resource.
- The tax rate should be optional by your own choice. Taxes from 0-90% or more would be great. And other political penalties which might render a starbase to be a full loss for the owner.
AND / OR
- Introduce politics where the owner of the territory will be the owner of the starbase (built by another civ), but you must negotiate a rate of sharing the resource and economic gains.
- You should also have to negotiate before building military and influence starbases in another civs territory. If not it's an illegal act, and might trigger a war.