Dooku is easiest to deal with when you target him last.
All putting the omega on him does is make it so it's harder to kill him in the harder way to kill him.
Basically the omega is kind of worthless. If not putting him in stealth would make people attack him faster, then it would be worth something. As it is, all it does is ensure that the enemy will attack you in the way that's right for them (attacking Dooku last).
Basically putting the omega on Dooku has no chance of making Your team work better, but it will make the enemy's team work better.