You can stringify the JSON Object with JSON.stringify(jsonObject) and receive it on controller as String.
In the Controller, you can use the javax.json to convert and manipulate this.
Download and add the .jar to the project libs and import the JsonObject.
To create an json object, you can use
JsonObjectBuilder job = Json.createObjectBuilder();
job.add("header1", foo1);
job.add("header2", foo2);
JsonObject json = job.build();
To read it from String, you can use
JsonReader jr = Json.createReader(new StringReader(jsonString));
JsonObject json = jsonReader.readObject();
jsonReader.close();