First off, I don't know if I am supposed to post here, as the rules say "any player may reply to topics" which I guess this counts as?
Secondly, wouldn't it be possible to set up private warps to villages and with GroupManager just give owners of the village access to those warps. I'm pretty sure that you can give permissions to people as well as groups with
/manuaddp [player] [permission]
I see where you are coming from though, about it being a hassle to set up and keep maintained, but I think you could use the custom commands plugin you have to create a simpler command to add village members which would both add them to the village, and give them permissions to the warp for that village. I haven't personally played with the custom commands though so this might not be possible...
Again, not sure if I was supposed to post this here, but just thought I would bring it up as it is relevant to the topic!
Luis