I think the choice of the term "affirmative defense" is poor. It doesn't really apply when determining probable cause to search or arrest. It is a term applied to the burden of proof once the matter is in court. In criminal law, there are very few true affirmative defenses. In most instances, a defendant has to make some showing that a defense exists, such as insanity or entrapment, but not to actually prove it. The burden is on the state to prove beyond a reasonable doubt that the defendant was sane or that police did not entrap the defendant.
Once there was reasonable suspicion to conduct the pat down, it makes perfectly good sense for the officer to inquire about a concealed carry license. If the suspect does not produce one, it is logical for a police officer to assume he or she doesn't have one and this forms the basis for probable cause to arrest.
Other than the poor choice of words, I think the Florida AG is 100% correct in pursuing it as she has.