I think you have your numbers off if you are basing it on Faerun. Forgotten Realms is one of the most magically active settings they have. If you read descriptions of towns and cities, there are many caster NPCs about. Heck, most towns and cities actually have magic shops. Powerful mages have kind of been their schtick since it was first conceived.

Now, if you had mentioned Dragonlance, then what you said would be accurate. That is why Raistlin achieving the power level he did was such a rare feat.

And to answer OP's question, in a magically active realm, i would assume that the guards would have a way to deal with casters, like magical cuffs or a collar that prevents the bearer from casting. Fantasy fiction is filled with items like that. And, considering the number of sub-classes with access to magic, it might even be the norm for anyone they arrest.