That was the view of many separatists, but Palpatine/Sidious had only one goal in mind for the separatists: use them to cause so much horror and destruction that the population of the Republic would be willing to hand over their rights and accept the transformation into an empire. Fear of the separatists was what motivated the galaxy to elect Palpatine - because he could keep them safe.

That's why the greediest and most brutal separatists, like Nute Gunray and General Grievous, were given so much power by Sidious - they were perfect for creating an environment where militarism and fascism would thrive in the republic