Separate Exposed Filter Widgets
Ok, so I realise that due to the fact that the exposed filters are on one form, it will be difficult to separate the rendered elements. However, I ran some tests using jQuery to  reposition the sort elements, and so far it seems to work using the following:

jQuery(document).ready(function() {
  jQuery('div#edit-sort-by-created').appendTo('#custom-sort-block');
  jQuery('div#edit-sort-by-title').appendTo('#custom-sort-block');
});


NOTE: This breaks if Ajax is enabled in the view, but that can be circumvented using the jQuery live() function I'm sure.

It certainly isn't pretty and definitely is a hack, but it will have to do for now. I won't be marking this as the answer in the hopes that someone can suggest a more elegant and Drupaly way of accomplishing this.