I agree about this.. in a battle today I had to rush my cav into position and attack so that my supporting army wouldn't get themselves massacred.
Of course, I forgot I was on the defense- the supporting army moved into defense position- and my cav ran over the enemy army anyway, but still- I dread fighting a battle with comp controlled allies, because there is a lot of potential for the computer controlled family member to die. I often even move them away so that I will have control of the other army myself!

I suspect CA will be fixing this. Have no fear, people, and enjoy the good parts of the game!