Actually I dont know of any scripts, or actions for Gimp, or Photoshop that will crop to a specific shape.... unless its rectangular. Same goes for batch actions in Gimp, and GD lib.
Truth is it would be pretty simple to do in Construct using the inverted alpha of your circle as a sprite.
You can apply the erase fx to the sprite then paste the image, with the sprite overlaying it into a canvas. You could then copy from the canvas to the image manipulator, and save it.
Setting up the batch for that should be pretty strait forward.