Hm, I'd have to see a specific example of where this is the case, since as of many versions ago that's already how it works. A previous target that changed factions is no longer targeted automatically. From what I can see, the only reason that could happen is if you targeted a space rather than the bot, in which case it will always re-target the same space regardless of who the occupant is at the time. But I just tried the exact situation you describe and it correctly switched to the non-allied target.