Yeah, sth needs to be done about those mines.
Good idea about reprogramming mines... nice (has sth evil to it: "Hey, the mine which destroyes my level 10 Marza was once placed by me...!").
I would prefer something like a mine control center. Each mine control center can sustain 10 mines. Every grav well can handle up to 10 mine control centers. Those centers can only be detected by scouts. Once a control center has been destoyed, the mines it controled will explode, too. No mine spamming anymore and a just conquered grav well can be cleaned in a reasonable amount of time.(Hm, Advent could just take those mine control centers over, once their scouts have detected them...? Hehe...).
And in my perfect little world, those mine control centers could also function as long range detectors for star bases: if there is a star base with long range weaponry in the same grav well, it can utilize the centers and shoot into their mine deploy range if an enemy ship happens to fly into it... (like scouts, who don't trigger mines...)