I will admit that the hero mechanic is a bit gay but I appreciate why it's in the game. For one thing, if heroes didn't exist you'd have no way to scout the map without wasting precious turns or putting your army in mortal danger. As far as I know the assassin unit has been in every Total War game anyway.
There are a few ways to deal with it. Many heroes can reduce the chance of a positive outcome for the enemy assassin just by being part of the army. Many heroes make great assassins themselves so they can just assassinate problem characters for you. Finally, most of the time LORDS, especially high level Lords are only temporarily wounded, meaning that you only have to wait a few turns to use them again. In that way it's just like a penalty kill in hockey, which seems fair.
Maybe most importantly, if a hero is separated from its parent army, then it has no use in combat whatsoever. Which is why most the time the player won't use them for that purpose.
Would you rather have a 50% chance to assassinate an enemy Lord before a battle, raising your chances of success? Or 100% chance of bringing your hero into the battle, and the opportunity to create your own success? I rest my case. And 50% chance is pretty lenient for most high level enemy characters that you would even care about assassinating, a lot of the time it will be significantly lower than that. I'll just take an extra hero on the battlefield thanks.
Besides, the computer is really hurting their own economy by having a million heroes anyway. Each one increases your global army upkeep quite significantly and each hero action costs resources. This quickly adds up. But having your characters wounded or occasionally assassinated costs you nothing in raw resources, and is usually a minor inconvenience at best.
So like I said, annoying but balanced.