If Amidala had been captured or killed, Palpatine would have been in a position to play the role of distraught native of Naboo whose homeworld had been illegally seized while the Chancellor did nothing to prevent it. Odds are, in fact, that as Sidious he would have arranged to make sure something terrible did happen to Amidala if she'd been captured so he could play up the tragedy for all it was worth. He would have made the rounds, the Senator in exile, unable to go home, mourning the loss of the beloved young Queen due to the loathsome acts of the Trade Federation and the spineless inaction of Valorum.
In the film, he makes a big deal about getting her captured and being forced to sign the treaty, but that's during the period when he doesn't know she escaped--so the "get her into a position where she dies rather than sign a treaty" plan is still in effect--and then after she fled Naboo and it wasn't certain where she was or where she was going. If she threw in the towel and just ran, that would have been a problem. It's obvious from his manipulation of her on Coruscant that he believed she'd not back down; had she been captured, she'd have died rather than give in and probably would have been killed. This works into his plan. But if he misjudged her and she'd just given up and went into exile, that likely would have been a disaster to the human population's morale on Naboo and they probably would have just folded, ending the crisis, and losing him sympathy in the Senate. Having Maul capture her and hand her over, where a tragic "accident" could have been arranged, gives him the martyr he could use.
When she shows up on Coruscant, clearly not backing down, well, he doesn't need to go through the whole fiction of the treaty any more. She's manipulated into calling the non-confidence vote, and then is determined to go back and fight. Now he sends Maul to deal with the Jedi and her. If she dies in battle, he gets the sympathy vote, and without her and the Jedi, the Trade Federation is likely to succeed with their invasion, but Naboo is likely in open revolt, and the Trade Federation has already been ordered to begin executing Naboo leaders, so he gets an ongoing crisis he can use to ride to more power.
Anakin and Obi-wan end up being the flies in his ointment: while the crisis gets him elected Chancellor, Anakin unintentionally causes the complete and total failure of the Trade Federation armed forces, while Obi-wan manages to kill Maul (well, so everyone thinks for a few years, anyway), so Amidala lives and is victorious. This ends the crisis, so Palpatine's consolidation of power is stalled out until a new crisis comes to a head with the Seperatists. On the bright side, there's this Anakin kid who seems potentially useful...
ADDENDUM
Maul acting openly on behalf of the Trade Federation also works into the initial plan; not only do you have the Trade Federation committing atrocities (which Palpatine can use for PR reasons), they're clearly aligned with the Sith. As some point the Sith would be revealed, but doing so on Palpatine's schedule means he's got the Jedi looking over that-a-way, toward the people acting against the Republic, while he's working at consolidating power in the center of the Republic, right under their noses.
