Proof of concept for encapsulating comments in a JSON string, then cleaning it out on the client side.

comments.json

jsonp123(
{
   "//" : "Here comes the callback",
   "callback": {
      "//": "This has the first item",
      "item": {
         "title": "Databases",
         "content": {
            "item": {
               "//": "Here's where the content is",
               "ID": "13254",
               "Technology": "Structured Query Language",
               "Acronym": "SQL",
               "Dialects": ["SQL-86", "SQL-89", "SQL-92", "SQL:1999", "SQL:2003", "SQL:2008"],
               "meta": {
                  "//": "Glossary section",
                  "para": "This article is about the database language.",
                  "GlossSeeAlso": ["San Carlos Airport"]
               },
               "ref": "markup"
            }
         }
      }
   }
}
);

recursive_json_comment_splice.js

function recurseSplice(obj){
  for (var e in obj){
    if (obj.hasOwnProperty(e)){
      if (e == "//") {
         delete obj[e];
      } else if (typeof obj[e] == "object") {
        recurseSplice(obj[e]);
      }
    }
  }
}

transfer_original_and_commented_json.js

$.ajax({
  dataType: 'jsonp',
  jsonpCallback: 'jsonp123',
  url: 'https://gist.github.com/raw/881674/fac4825d287abcf0c92b1216e6a05b747fa140d1/comments.json',
  success: function (data) {
    var call = $.extend(true, {}, data);
     $.getScript('https://gist.github.com/raw/881674/ab4ae809ce434d4c9e679d4917dc9610e8906abd/recursive_json_comment_splice.js', function(){
      recurseSplice(call);
      console.log(data, call);
    });
  },
});