Absolutely, Order 66 was an act of mercy.
For over a thousand generations the Jedi blatantly and pridefully forced their rule and religion upon the entire galaxy. They maintained unquestioned control over countless members of the senate, and directly controlled many planet's governments. They acted as manipulative ambassadors who could control communications between worlds. They were the interstellar police force for the government, given the right to kill their enemies on sight without any question of their authority or motives. All the while, they refused any oversight from outside sources. They had no checks, no balances. They wielded untold wealth beyond that of any planet (enough so that an entire interstellar army could be hidden in their accounting without anyone ever noticing). They even controlled the maps of the stars. The Jedi called this form of government "democracy".
The entire clone/droid war was an act of mercy, designed to create a conflict with minimal risk to the citizens of the Republic. By fighting a war between machines and clones, Palpatine saved an entire generation from the conflict of war. Order 66 was the end of a merciful, masterful plan that removed the Jedi with the least violence possible.
