ok well before doing that I'll post this:
setenemy F F X Y - Set a faction as enemies with another. (F = faction ID, X = 0/neutral or 1/enemy, Y = 0/neutral or 1/enemy)
May need to be used in lieu of just upping rep (also probably for the sub factions when I look them up in a second)
For example:
setenemy 0001B2A4 000EE68A 0 0
In this case "0001B2A4" is the player faction and 000EE68A is the legion. Not sure if it matters if it is first or second. This should set overriding enemy flags off. If that command does not work (and neither does reversing the order) then go ahead and repeat it with the "player" faction and each of the following:
0012677F
00137324
0013ACAB
001252C7
00154418