One guy with a gun can hold a bank full of people hostage. Even if there are several dozen men with guns outside. They guy trying not to fight always has to have massive fire superiority over the guy who does want to fight.

The Trade Federation deosn't really want the fight. The droid armies are supposed to deter the Republic from opposing them. The Republic is using the clone army as a tool of naked political agression. They will forcibly deny the right of secession one planet at a time.

As long as the Trade Federation members are just in it for the money, they lose this battle of wills. War is bad for business. Unless you're just selling weapons to both sides. Like the cloners.