I'm not sure this a system that can be changed in a way that won't impact innocent players negatively. The issue is how easy it is to build these safe palis, and the lack of a penalty for using them. There's pros and cons to any change you could put in place, and the pros and cons always vary on which side it's going to benefit and who it's going to hurt.
Current system: Group runs into safe pali they own, visitor debuff prevents anyone from following in.
Proposed Change : Gate is visitor coded (such as Community Fair) innocent players are now guaranteed to be ganked due to their inability to run to safety in these areas. If you aggro someone outside, they're toast. Safe Palis will just switch their gates to not visitor coded, and carry keys. Upon running in to your safe pali, they can just close the door behind whoever follows them in - where they are either outnumbered, or more people are potentially hiding in the house to pop out and down them. Not to mention the risk of building catapults inside these safe palis now, making it even more unsafe to follow them in because you risk being downed and catapulted to death.
The problem is how easy these PClaims are to drop, how cheap they are to maintain, and how difficult they are to remove.
This issue will probably require a reexamination of personal claims, or the siege system, to resolve. Back in Legacy you just dropped a ram, and eventually you'd find a window of time where it wasn't checked and you could break in and take it over. I'm not going to invest the current amount of siege time it takes, to remove a safe pali that can be rebuilt a day later by someone who spends the 5 minutes neccessary to build a palisade and a pclaim.