Well this would probably be a more feasable suggestion than making a public safe HQ mine, I assume the mine foremen are selling bases and not functional mines, if so, good for the faction.
Make a few classes of mines, a Non functional mine usable as a base, a mine with average deposits(those who fear those who do not keep their hands in their OWN pockets), and a mine with HQ Deposits. Now I would honestly make a highly functional mine cost more than a farm, as it is probably rich in HQ Deposits, and probably something a faction member with high Charisma and speech would have to talk the foreman out of hoarding it.
Rather than having gangs live in caves their whole life, don't put anything but ore and mineral deposits in the functional mines, and don't make them count as bases, but rather as Assets, and allow factions to own say, a single functional mine. Of course, owning a functional mine costs more than moving into a depleted mine.
If someone wants a safe place to get HQ ores, they should pay for it, safe HQ mines should be hoarded, and maybe even cost a million caps(as owning such rare deposits is like owning Fort Knox), no that isn't a joke, if a faction wants a safe place to mine HQ deposits, it's going to have to leave their wallets empty or near empty, also consider limiting the amount of safe mines, new ones only opening up when one has been destroyed(using dynamite to cave it in), and even then they open up a good while after the mine has been destroyed, of course, HQ mines won't be easy to find and destroy.