Some things I learned while preparing for my mini game (sadly preparation took much longer that I thought, and it might still take a bit, since I found some issues, though that will be in new sub-forum).
Old logins system for GT totally sucked. And it is simple (relatively) to setup proper freeciv login (I'll be using that). Freeciv can use on of server db backends for account storage, I'll be using sqlite, though for GT probably mysql is better choice as I presume forums are already working on it. Freecivs account db, only use two tables, one for tracking login times/attempts. And one for authentication, that is basically user name and I think sha1 hash of pass (or maybe it was md5, will have to check on that). Not sure which hash forum uses, but in any case one could quite easily write required account names and hashes into freeciv tables from other program. Thats for authentication setup.
For game setup, well you should only need rulset. Which users can agree up and manage whatever way they want (say using github). Then when they thing everything is setup you checkout ruleset, start game server with it and auth db. And that should be basically it. Quite little involvement needed. Frankly original GT system with server console and stuff seems like a bit of over-complication. If we were to play random games with random starting nations (the best kind of setup

), rule-set to be checked out should be mostly enough (as basically all settings can be set up in ruleset, exception being probably being some server settings which should not vary between games anyway and could be copied from old games). Well with hopes that in game adjustments are not needed...
If one is very afraid that malicious ruleset causes buffer overflow and arbitrary code executions, well dunno start freeciv with that ruleset in vm first?

But this sounds a bit paranoid, though
