The answer is two-fold:
1. Get your mind out of the Third Age. The mod is set 200 years later. Think of the history of our own world. We were at war with France 200 years before we were allies with them in facing Germany.
2. We will aim - where possible - to lessen the severity of the diplomatic breakdown in relations pending finding ways of doings so (it's pretty much hard-coded) and pending the release of the storyline of the mod which, for all you know, may have a very good reason for having Rohan and RK at each other's throats.
Be patient. Enjoy the game