Getting PvEers flagged is amusing.. I remember many evenings of amusement at tricking people into flagging and then destroying them 3:1.
Way too many people use multi-target attacks without realizing it, and that opposing faction flagged player that jumps right in front of you mid combat while you're multi-targeting.. yeah, that gets you flagged fast.
Personally, I prefer what Rift does. If you don't have pvp enabled, you can't attack a pvp flagged npc or player that would cause you to be flagged. There's more to it but it eliminates most of the "oops" out of flagging.