Amber,
   Sure the code that need to be changed is in the jimu.js/LayerInfos.js _getLayerTitle function:
notice lines 8 -27 are commented out to prevent the adding of the service name to the layer title.
    _getLayerTitle: function(layer) {
      if(layer.title) {
        return layer.title;
      }
      var title = layer.label || layer.name || "";
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      return title || layer.id;
    },