Can't help but feel your problem(s) was due to another mod conflict. I've played this quest at least 4 times in FO3, plus once in TTW too, and always peacefully resolved things, got Iain home and the two factions working together. And they've never once turned on me. And during these times I've never once seen a raider near Arefu or the family. Maybe you should steer clear of mods adding raiders/enemies?
The ONLY time I've ever had a problem is when adding mods to Arefu, and one other unrelated mod (which I forget, to do with traders I think). So I always steer clear of any Arefu mods until after this quest - which works well because they then seem like with it's dispute solved Arefu is growing again.
It's not a mod conflict. I've had the same problem as the mod author and I don't even use mods that add enemies. Fallout 3 is just really f*#@ing funky.
the problem with original scripting is if they die they will attack you. not if they are killed by you. if a raider would kill any of them they blame you. in my mod i changed this so they only go berserk if they are killed by you.
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The ONLY time I've ever had a problem is when adding mods to Arefu, and one other unrelated mod (which I forget, to do with traders I think). So I always steer clear of any Arefu mods until after this quest - which works well because they then seem like with it's dispute solved Arefu is growing again.