Hi Toby,
You can use the GF filter that let's you assign choices to checkboxes, and iterate through the list of categories in that function. Then you can prepend a dash or non-breaking-space for lower levels (recursively, for multiple indents). The checkboxes will still be lined up with each other, but the labels/answers will be indented.
Alternatively, if you aren't planning on changing the categories, you can target them with css individually by the unique classes in their divs (e.g. gchoice gchoice_3_44_3) to indent the checkboxes themselves, but that would be tedious!
Aaron.