The game fails if it doesn't force everyone into the deep end of the sandbox. Outside of living under the protection of the remnants of the [insert nation] Military (neutral NPC faction) under harsh restrictions (skill caps, clothing/weapon restrictions, resource tithes, crafting restrictions (no structures/ fire arms) everyone should be flagged outside of a Military zone of control (tutorial/neutral areas). Seeing as there are no levels, this is completely viable, but it limits your scope of the game severely. Not only that, but you're essentially a trade slave and living in a refugee camp (until the camp hits a pop. limit and upgrades to a new tier making it an increasingly fatter raid target) and prone to being shuffled around safe zones.
Factions are fine, but the flagging system from SWG was a failure. If you want to stay neutral or prevent the game from turning into DayZ DM, create the framework and force the social network and community into existence. Mercenary body guards (SWG Bounty Hunters) / friends or die. In an apocalypse you either live self-sufficiently and secluded or you have friends or you make a transaction for protection. There's no other way around it.