Not really, the Empire and HE will certainly fight when their interests conflict.
The natural allies tendencies are carried out through the diplomacy modifiers based on alignment (Lawful civs get bonuses with other Lawful civs, and penalties with Chaotic civs, etc), Religion (so Salvation civs Empire, Kislev, Bretonnia, Estalia and Tilea get bonuses with each other and penalties to others, etc) and council membership (so Alliance civs get bonuses with each other, and Covenant civs get bonuses with each other).
So, there are already strong tools to encourage enemies to fight each other more, but this is still warhammer, so we definitely don't want to prevent any conflict between some teams. We've debated adding a few more (so that High Elves and Dark Elves aren't fairly friendly because they share a religion, and so that Dwarves and High Elves aren't too friendly from both being lawful), but mostly the current system is ok.
I do think we need to add in Permanent Alliance functionality, probably given with the lordship tech.