In my B5.3 game I resorted to buying up a minor's constructors as they were built to prevent the problems outlined above (minor's bases prevent my econ and mining starbases in my ZOC). Usually I could trade a tech or two for the minor's constructor, so this did not cost a lot of gold. Then I used those constructors to build econ and mining starbases for me in positions of my choosing. It may be a long time before those bases get boosted, but at least it kept the minor at bay.
In another game, the minor still snuck a mining base into my ZOC that prevented my doing an econ SB for Earth. That time I was able to actually buy the minor's SB with techs and gold. Then I destroyed the SB and immediately created the econ SB I wanted for Earth with my constructor. It was after that experience that I started trying to trade for minor's constructor if they were close to my territory.
I like the suggestion above that minor's SBs be limited to some set distance from their homeworld.