As the resident Local Militia expert, I'll get this one...
Go into the GalaxyScenerioDef file (in Gameinfo folder)
Go to almost the bottom of the file and look for "Planet Default Setup" (or something like that), and choose "empty" for all the planet types that you want to have no local ships.
Also, near the top of that file are the "orbit body types", that contain default militia setup pointers.
The whole thing is interconnected...
The map planet types point to the planet entity (orbit body) types, that in turn point to the default militia setups (which can have a level of abstraction applied to them, making it just plain silly at times)...
If you make certain planet types point to the "empty" militia setup, then those planets will not have militias. You can also make new militia types and planet entity files if you want to make a completely different type of militia spawn randomly at a specific planet type (with no spillover of you do it just so).
My Confluence Militia Mod is a good place to start if you want to do drastic changes to the Stock SINS local militia setup... ...or if you want to to try to implement several non-related militias all randomly occupying Terran planets without mixing forces...
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