Maybe have a minimum member count combined with activity count (entrances/exits logged to a counter) to assess how "hot" a base is.
The "hotter" the base, the more detectable it is.
As for TC/loyalty, have the "left alone" timer be sort of like the base-activity counter.
One representative popping in now and then isn't going to do it, but perhaps the equivalent of a full TC countdown spread over each day instead of all at once (x number of unique gang members from controlling faction talking to TC guy per day).
If the quota is not met, influence decays at a greater than normal rate.
Militia pay would be perhaps 1/10 of pay for equally powerful mercenaries.