Krumlov is wonderful. Especially in the morning and evening when most of the tourists leave from their day-trip. When going there definitely stay overnight and be surprised by what that small town has to offer.
My recommendations for gluten free places to go to:
Laibon
Laibon is the only vegetarian restaurant in Krumlov, they have a lovely outdoor seating just right next to the Moldau. The staff knows very well about gluten and you can have every meal from their menu (even the dishes not marked with that G in the circle) - they will make it gluten free for you.
It is very tasty and healthy - thumbs up!
Bulldog‘s Papoo
You will also find a little snack bar close to the mini market called Bulldog‘s Papoo. They offer a gluten free cheese burger - so if you’re craving American food, go there!
Stall close to the library
Sorry for the bad quality - only had a screenshot of a video I posted.
In the inner courtyard of the library of Krumlov called Mestska knihovna v Ceskem Krumlove you can find a little market offering souvenirs and gluten free and vegan snacks! Cookies, Energy balls and other healthy treats - all made from nuts, dried fruits and seeds. Ask the owner for details.