I feel like it might be a good idea to gradually decay the drillers and/or shields on inactive bases.
We had someone drop out of our game on the 2nd or 3rd day who didn't do much in the beginning, but had 3 factories that continued to produce until he resigned. This resulted in factories with 70+ drillers and 20 shields before he resigned, which for the majority of the game was pretty unassailable even though nobody controlled that space.
I was adjacent to him and am just now in the process of taking over those abandoned factories at day 6-7. Even then, it is of questionable benefit and I probably just should have used those drillers to build another mine. It was actually more beneficial for me to have a 'wall' on one side of my territory that nobody wanted to bother going through for most of the game.
Decaying things back to a neutral state over time seems like it would be a reasonable way to approach that and make sure the space was reclaimed and utilized for gameplay.
(P.S. For some reason, when he resigned a gray/captured thief started heading toward my nearest base in an empty sub and did nothing when he arrived. Not sure what caused that.)