It was a false attack, red herring, misdirection. Militaries have been sacrificing grunts for the sake of a greater goal ever since there was a chain of command. To find out the answer to your question, you'd have to ask...
What would the Trade Federation winning have done to improve Darth Sidious position?
What would the Trade Federation losing have done to improve Darth Sidious position?
Both had the same goal. To gain the power of Supreme Chancellor. He becomes this while the fighting is going on. Who wins now no longer matters, because now he has access to new resources to further cement control.
If the Trade F wins on Naboo now, Palpatine can call them traitors. Go to war now or otherwise delay and later go to war with a clone army.
If the Trade F loses, help rebuild Naboo. Gain confidence of good senators and others who he doesn't control. Eventually lead it to the clone wars.
In both cases, Sidous avoids detection, gains absolute control, and systematically destroys the Jedi. It was pretty much set in stone the moment he became a senator. Everyone is so wrapped up in the peaceful life they didn't even think there was a problem til it was way too late.