Sorry, I know it's very inconvenient that you can attack people from the same allegiance, but I wont increase party size.
I guess you can consider this an extra challenge to the toh mass battle, having to be careful not to hit your own people. Same thing in woe if you have more than 1 party not from the same guild, gotta be careful.
Since both side had 2 party they both get equally affected by this problem. I know it's a pain, but sorry you will have to deal with the game constraint.
