The Republic is a big giant corrupt beurocracy! Padme and Naboo should know this better than anybody. Because it took the Senate so long to act their planet was nearly overrun by the Trade Federation forces.
So why would Padme and Naboo side with the Republic. Why wouldn't they join Count Dooku? Why would they choose to side with the Republic led by the creepy looking Chancellor Palpatine?
Why would Padme and Naboo agree to clone people, which would seem wrong I'm sure to a sweet girl like Padme, just to stop a few hundred solar systems from seceding. What would she care?