As a solution to a problem the idea has some merit but it shouldn't be a problem and the notion that there is a problem is sort of problematic.

If China invaded Cuba, America would respond.

There wouldn't be a debate about why America responded or some secret plot to maintain a force to defend Cuba from China.

America would do something about an act of aggression on it's doorstep regardless of the history it had with it's neighbour.

Same with the Federation/Confederacy.

i would have the Confederacy declared in the first film and have other planets attacked at the same time as Naboo.

The army should be in response to violence not to the desire for separation (the current PT is obsessed with keeping the Republic whole rather than keeping it safe) and so far we only have one major act of aggression.

That way you don't need any debate about if those actions should be responded to only some debate as to if a brainwashed army of purpose grown slaves is the way.

Also wouldn't it be easier to sell the idea to the Senate if the people of the army reproduced via cloning already anyway (maybe they are genetically sterile or have some cultural taboo regarding conventional reproduction)?

That way the ethics boil down to the issue important to Padme, limiting escalation rather than what amounts to child soldiery.