OK. I've avoided this since the "license" came about.
To answer the original posters Q. you can get a license at Tres Pescados. North end of Front Street, nice guy, trying real hard to promote C&R flyfishing(and other methods). He's got a great selection of local flies, and equipment, and can book you guides. Whoever the guide is he'll pick you up wherever you're staying.
But frankly. I'd challenge someone to tell me they had a licensed guide that said, before you climbed aboard, "do you have a license"?
The C&R is a great goal, where needed. How many Tourists are bringing in stringers of bones, tarpon, or permit?