Hi,
Sorry for the late response, some tickets got spammed, and I just noticed it on the dashboard.
Well, the only possible solution I can see to this matter is to create 2 search instances:
Search 1: A search bar only, without any filters. This is going to be used as a free search.
Search 2: Filters only, this is the search you already have. All you need to do is disable the input on the Layout Options -> Search box layout panel: http://i.imgur.com/Ln9bE8t.png
Then place the two shortcodes one after another and it’s done.