I don't support this idea, mostly because there is already an established rule to fix this; 6.10 (player ID and reputation should match actions)
Granted, it (6.10) does provide extra work for the admins and *cough* it isn't sanctioned often enough *cough*, I still think that forcing something like that will kill certain roleplay and there are way too many possible interactions that would simply hit a brick wall because of an in-game mechanic.
I asked this earlier about Chrysanthemums on lawful bases in Liberty for example... Who would have thought about things like that when deciding all of the ID/docking restrictions?
Sadly the current gameplay mechanics don't always coincide with roleplay, if something like this is doable, I'd like it to be trialed on military bases or other secure sites first to see what happens.
EDIT: Also Guard bases should only be for those in that faction, guard ID or normal.
It's done so on Hamburg City Server. One cannot dock with a Clan base, untill the Clan leader allows them to, that is, hacks their reputation to full green.
Other than that, the base just doesn't allow you to dock. You stay stuck in space. There was a bug, I don't know if they fixed it tho. Whenever someone tries to dock, and they can't, the base is stuck and nobody can dock for some time, I don't know how long. My friend and I managed to block a TCE base that way, once... Noobs we were:D
Anyway, it's possible
Simple solution: make repninja autohostile to all guard bases, save for your faction. Make bases of some specific factions that require these services guard bases, not normal. That way, an admin intervention is required to address the issue. Tho, I believe a console command is possible to make for that also.