Not sure. Looks like it was handled "The Chicago Way" whether locally, or nationally =(
Chic-fil-A uses a non-traditional franchise system. Corporate Owens the store (land/building/lease). The employees are employees of corporate. The franchise holder is in a profit sharing agreement with corporate and acts as the “face” of CFL in the market.
The agreement that disclosed the change in policy was signed by the Director of Real Estate for CFL. It states that it ( via the charitable arm) will no longer fund the 2 charities that were listed in the dust-up over the summer.