Use jq to first sort all keys. Then diff to do the diffing:

jq -S . A.json > A-sorted.json
jq -S . B.json > B-sorted.json
diff A-sorted.json B-sorted.json

The above example is for Linux but both jq and diff is available for Windows. It seems Windows has an alternative diff tool called fc, perhaps this could be used instead of diff.

I found the problem as I was typing this up and thought I'd post the solution in case anyone has the same problem. I was sending my left and right as json strings, not objects the fix was to parse them to json objects first:

Copy    window.renderDiff = function (left, right, element) {
      //parse to json object
      left = JSON.parse(left);
      right = JSON.parse(right);

      var delta = jsondiffpatch.diff(left, right);
      element.innerHTML = jsondiffpatch.formatters.html.format(delta, left);
      jsondiffpatch.formatters.html.showUnchanged();
      return element.innerHTML;
    }

If I understand the question correctly, the following should do the job. I'll assume you have access to jq 1.5, which includes the filter walk/1 (if that is not the case, it's easy to supplement the file below with the definition, which can be found on the web, e.g. the src/builtin.jq file), and that you have a reasonably modern Mac or Linux-like shell.

(1) Create a file called (let's say) jq-diff.jq with these two lines:

def sortKeys: to_entries | sort | from_entries;
walk( if type == "object" then sortKeys else . end )

(2) Assuming the two files with JSON entities in them are FILE1 and FILE2, then run one of the following commands, depending on whether you want the JSON entities within each file to be sorted:

diff <(jq -cf jq-diff.jq FILE1 | sort) <(jq -cf jq-diff.jq FILE2 | sort)

# OR:

diff <(jq -cf jq-diff.jq FILE1) <(jq -cf jq-diff.jq FILE2)

Brief explanation:

The role of jq here is to sort the keys in the objects (without sorting the arrays) and to print them in a standard way, one per line (courtesy of the -c option).