To prevent your brother from attacking PES Ekudu all you have to do is target it yourself and hit shift I, it should tell your brother to ignore the target. With any luck he will take out the other fighters. Do you have the latest patch(2.02). I know a problem was fixed in one of the first missions. I myself have never had problems with the Ekudu on that one.
"Dulce bellum inexpertis."
(Sweet is war to those who have never experinced it.) Roman Proverb