So let me see if I got this right. You AoEed someone that can counter, and upset he did what is skill intend for him to do, counter when being hit?
Let me give you some advice, you see dooku, or a ima gun leader Jedi team DONT FREAKING AOE THEM, THEY WILL KILL YOUR TOON. Counter toons are in fact a counter to AoE toons. Just like sid is a counter to jedis.
Dooku gets bonuses when he attacks outside of his turn ( ie counter attack ) to include gain turn meter, so don't give him a reason to counter attack unless you just have to. I have seen my dooku at full turn meter get attacked, then counter, then attack, and able to attack again as he ended up basically having 2 full turn meters. While it only happened once it still made me happy as the ai does this constantly to me and I for once got my revenge