Once Sophie stops to think before judging the scarecrow, things begin to fall into place. The scarecrow initially seems like it’s on the side of good; if it's looking for “parts,” the implication is that it’s working against the witch to possibly undo whatever she’s done with regards to assembling Percival. Additionally, the scarecrow confirms that Sophie “talked life” into it, highlighting that Sophie has been powerful for some time now and just didn’t know it. And Calcifer, at least, has empathy for the scarecrow. Further, Sophie trusts Calcifer, so it seems more likely that the scarecrow isn’t actually evil.