If you use your nightsisters I believe you still have access to the event ability that lands daze on Dooku. It still takes a year to beat him into submission but if you daze him you're good since he won't be able to counter and regain protection. You could even run a normal team and put Asajj in the squad to get the daze ability. Also you could use a toon that lands daze. If you're running a rebel squad, consider putting Zeb in with CLS for the daze on basic.
Here are more characters with daze that you can bring in to prevent the counter attacks. Normal raid bosses are immune to daze but Dooku isn't even though he has a lot of tendencies of raid bosses in this event (immune to massive damage/annihilate, fracture doesn't prevent him from taking turns). Hope that helps!