This is my take:
Palpatine was going to use the takeover of Naboo to set himself up as a sympathetic figure in the senate. With his people veritable prisoners he would then get a conspiring senator to call for a vote of No Confidence in Chancellor Valorum.
Being the quick thinker that he is, when everything wasn't going exactly to plan, he manipulated Amidala to call for the vote instead.
Notice that once the new vote has been set into motion, he no longer cares if Amidala lives or dies.
Quote:
Wipe them out, all of them!
The Federation, being pawns, were unaware of the shift in plan. So they were still trying to capture the queen.
Once he became supreme chancelllor, I suspect he would've "convinced" the Federation to leave Naboo. This would make him a hero, and actually help to consolidate his power faster.