I do not think there is anything configuration wise you can do. You will need to get the count for the dimension then add your own logic for going over child dimensions and subtracting any values.
You might consider running two queries. First to get all products and refinements. Second that has a filter set to remove Out of Stock products and from these results gather the bin counts. This second query could be super slim for performance - 0 results, and perhaps asking for only the refinement counts for specified dimensions (available in the 6.4.x and possibly 6.3.x APIs).
An alternative is to change the User Interaction model so you only show in stock products - thus no need for extra computation/queries. And have a link or some UX component that allows the user to see out of stock products. We often do something like this:
Initial Query is for in stock products ONLY
if no results returned, relax the query to say partial match
if still no results, relax query to get out of stock products
if results, display to the user something like - hey we don't have anything in stock that matches, but we here are some out of stock items...