Sorry to hear, though if it was a 'used' base beforehand, it is a bit difficult to 'sanitize' it as you so put it. This is the inherent problem with buying any used base in this game, and given that, if you can afford a bunker, I would've personally had a legion of slaves/mercs there on the 'kill all' sort of orders for some time. Then again, I am paranoid and not everyone will go to such great lengths.
...Instead I just live alone in a base.
Much cheaper.
True, true.
It happened soon after getting the base, so mercs weren't up and running yet (needed to make new charcters to handle the mercs as other mercers were tied up at other bases, also without proxy use, escorting new merc alts to Bunker requires playing "Time Zone Tag" with other player(s).)
To sanitize:
Could delete all names listed in Terminal before sale/adding the new owners, Teleport those names to the Bunker, kill them so they lose base map.
It would be a lot of typing.