The system recognizes the value of the FreeShippingThreshold appconfig parameter as a global certainty; as long as the cart subtotal is $50 or greater the user will be offered the option of free shipping.
What you could do though is go into the code where FreeShippingThreshold is being utilized and check for the existence of the coupon code. If a coupon code is being used (or if certain coupon codes are being used depending on how you are setting up your coupons) then don't execute the FreeShippingThreshold code that says "give the customer free shipping". Not hard to implement...will just take a few code modifications
<a href="http://www.aspdotnetstorefront.com">Shopping Cart Software</a>