As a workaround for using a camera & the puppet tool without the crazy glitches, I've duplicated the layer so I can keep the end position of the character and remove the puppet tool before the camera pans again.
Whenever I remove it, the character springs back to it's original position. Is there a way around this?
Once you remove those pins, you remove the scripting, so it won't keep it's position. I don't think there is a way to bake the pins. Try "save frame as" with an alpha channel on your pinned character and then import image as a layer.
I suggest designing the character in PS or AI in the position you want, or look up rigging tutorials. Puppet pin tool doesn't always give you the cleanest bends, so that's one way to ensure the best quality.