Going from "she looks like a dead person" to "she's an android simulacra of a dead person" is a leap of logic so great you'd need a navicomputer to plot it.
The Yaris natives were certainly manipulated. They're obviously supporting the rebels, and I don't doubt the Sith at least nudged the governor towards organizing his diversion.
With the GT, though, I'm going to apply Hanlon's Razor: Never attribute to malice that which can be adequately explained by stupidity. Of course, from our perspective, Clarke's corollary to the razor can be invoked ("sufficiently advanced stupidity is indistinguishable from malice").
Aside from the general incompetence that plagues every major government in Star Wars, the task force is being commanded by an FBI agent, not military officers, so I don't expect tactical brilliance.
On top of that, peacekeepers are always saddled by extremely harsh restrictions. Seriously, look up what UN peacekeepers have to put up with sometime.
It's almost like someone knew "peacekeeping mission" is code for "non-stop BS parade" and wanted nothing to do with it.