If they are able to prioritize zone entry to those from the world itself that would be a good thing, but I'm not sure if that would change anything if the zone is already full.
We periodically see this happen on Jenova when we get hunt trains in and everyone and their brother is doing them and normal Jenova players can't access those zones for our activities. That's brief, though, but it could also be that they're limited on what they could do server side if it's something they can't piecemeal implement on just one server. So something like the afk timer could be like that. We have seen them able to take down specific zones on specific servers for maintenance before so at least that is possible.
I find that unlikely, though, because nobody here is really breaking any rules of the game. They're using DC Travel for the intended purpose. So I don't see SE punishing them by taking the zone down and making them leave. I'm not sure what the solution is and not sure how much is in SE's power versus the community's power to work with the residents of the server.