Well, for one, we don't even know if there will be friendly fire/team killing in co-op mode. For 2, not sure how AFK people would even affect you, since they'd just load out when you left them.
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The afks won't be an issue in Destiny as they were in Reach's firefight, but I've played co- op campaign enough to know players will grief other players and they will do it at the most inconvient times. So I suspect someone will be camping a sleeping Hive army and pop a round into them when you're trying to stealth out of a situation or someone will be running in with a monster train behind them yelling choo choo.