The problem is that the seperatists and the Senate were both being run by the bad guys, hence an outcome favorable to the Senate and to the protagonists (Amidala, Anakin and the Jedi) was not achievable. The game was rigged.
Look at it this way: From one end, Dooku, the Sith apprentice, is working with the Trade Federation and other commercial guilds to get star systems to leave the Republic and build a huge droid army. Why? To create a threat to the Republic, per the instructions of the Sith master, Sidious.
From the other end, Palpatine is attempting to get the Senate to approve the creation of an Army of the Republic. Why? Ostensibly to “counter the increasing threat of the separatists” (a thread he and Dooku have created in the first place), but really as a means to further consolidate his power as Supreme Chancellor and, in the future, Emperor.
By simultaneously creating the threat and the means to counter it, Palpatine and Dooku (whose job security we can assume is severely limited) arrange things so as to suddenly have a military force present on thousands of worlds (which we see beginning at the end of the movie), under his direct control. Hello, Empire!
The wishes of the Senate, and the lives of our protagonists, are incidental to Palpatine. If his and Dooku’s plans to use Jango Fett and Zam Wessell to kill Amidala succeed, the Senate loses its strongest opposition voice and he pushes through the Republic Army vote. If they don’t, he goes with Plan B and gets her moved off-world so she isn’t present when the crisis comes to a head anyway, and he still gets the vote put through. Using Amidala’s proxy in the Senate, Jar Jar Binks, to boot.
The whole thing is Palpatine playing both ends against the middle, effectively taking all potential enemies out of the picture. He uses the clone army to destroy the droid armies of the commercial guilds, then installs them as an occupation army on thousands of worlds. Meanwhile, he’s now killed all but a few of the Jedi on Coruscant, diluting their power and setting the stage to wipe them out completely throughout the galaxy. He’s got the plans for the Death Star from the Geonosians, he’s got emergency powers from the Senate, he’s got a relationship with the Chosen One, and he’s got the Jedi unable to effectively use the Force.