Why are you approaching the problem from the arse's side? Make a guarded location for every town, just like mines. Or one for all of them. Or put it in the NCR. Post a terminal there. You want to enter BH, you pay X caps at the terminal and you get flagged as *paid* for a given town. You die there while being flagged, the controlling faction doesn't receive shit. You don't, they get 50% of the X caps you deposited at their TC stash after your "day pass" expires.
Suddenly:
- no alting can overcome the system - you pay from the gang stash, you lose 50% of what you paid for a funny flag over your head
- no stupid rules for TC people - they do what they want, militia works as it did - if they kill people indiscriminately, their paycheck's going to suck hard
- controlling faction becomes interested in protecting visitors, other factions might want to kill them to reduce the income
- the bonus cash stays when the town gets captured by another faction and flags are visible for everyone - so if the attackers are there to stay, they just might want to reduce collateral damage
- there's a clear distinction between hardcore PK, mild PK and friendly factions
- spies can still be killed on sight even if they use the system, it promotes real visitors with real business there
... good enough?
Oh, and the passes could come in all sizes and shapes, so a wealthy merchant could pay just enough for the gang to make looting him questionable... I mean yeah, you could get that armor and some wares, but he won't come tomorrow with more, right? If you make trading in TC-able towns more profitable than trading in, say, NCR - you could get some real money and ware transfer going on - or a player driven economy, if you will. I mean, Klamath could pay you more for EP based stuff while Gecko could use some brahmin hides. Endless possibilities.