There is a bug I have heard about regarding the disguises. Apparently you have to take them off, get out of inventory (be naked in game) then go back into inventory and select regular armor for it to leave. I have seen a few threads where people say this works to become un-hostile with said faction again but you have to use the same disguise you used prior (or perhaps the same type... dunno).
Hope this helps
I had equipped brotherhood of steel armor briefly before, but i tried this and it didnt work.