I have (maybe) solution for this alt abusing guild system.
My solution consist of 2 parts. Part of benefits from focusing on only one gang under one guild, and part of penaltie, if you dont focus on the one gang.
I will start with the penalty system.
Imagine, that your base will need water as basic resource. Every base will have (or maybe not every) its own water supply and water tank. Small caves will grant water for 5 alts per real day. If you log more alts, your water demand will raise and you will consume water from your water tank reserve. You will have 2 choices: use water bags to resuply your base or use water merchant (under the trade guild.. only they will have knowledge how to find water resources and transport it).
It is very falloutish... first half of fallout 1 was about finding water chip because water was the n.1 resource in the wasteland. (Fallout new generation (= "fallout" 3) was about water resources too).
Of course, there must exist penalty for lack of water. I can imagine penalty like base destroying, but i think that this is too much hard, but best penalty i can imagine is, if your base will have not enough water, your base will be visible on world map, until you will resupply your water tanks to some level. It was hard to imagine the relationship with real world with current problem (i know that this is game, but IMO there must exist some kind of relationship between game and real world), but i found it. In real world, if your hideout will be without water and the inhabitants dont want to die, they have to find water somewhere else, so they will oftem leave and come to the hideout and this helps scouts to find this hideout.
So point is, if you will have base with huge number of players (alts), you will need more water. Current system is bad, you collect money, buy base and nothing else.
Second part is about benefit, if you (team members) focus your attention to only one gang.
At first, i think that there must exist possibility to make regular base network under one gang possesion, with special rights system (for newbies,..). I can imagine 2 basic types of bases: crafting (+storages) and resource "base". If your gang will be bigger and wants to posses resource bases (like current outpost,...), you will be able to. But you will need to posses bigger crafting (storage base) to posses bigger resource base. And to have bigger base with bigger water tank, you will need to hold your basic base for some time, you will need to make some special guild quests.
The possibility of ownership bigger bases, better resource bases,... would be only one from more benefits that your guild offers to you. There should exist some rank system in the guild. If you reach first few ranks, you cant loose them, until your gang will leave the guild. But highest ranks, with best benefits, would need to periodically repeat some quests*, activities.
I can see 2 big problems: balance (but this is beta) and boredom. So i suggest that first few guild ranks should me NPC quests, but to reach and hold highest ranks, you will need to make only real player interaction quests*. I.e.: water merchants will need to supply X bases per week, PK raiders gang will have to attack x cities (or) and X water merchants caravans, PK mercenary will have to protect X water merchants, the crafter guild will have to sell x weapons.
Why i am suggesting this. From my own experience (VSB), there exist many players which were roleplaying traders, PK, anti PK, mercenaries, someone was pure crafter etc. etc... Current system is kind of self-sufficient gang economy. You have no need to trade with other gangs, or non gang players, because if you have need, you can make alt and problem is over. If you will have to focus all aim to your own gang, you will have benefit from this, and then you can trade these benefits with other gangs.
And look, now, we have almost useless Raider base (guild), in this universum, there exist water merchants, Brotherhood, NCR, ... with only one usage.. join, reach level 3 proffesion, leave then (if you can). So the background for guild system is already exist.
