Preheat oven to 350 and line a standard 12-cup muffin tin with muffin liners.
In a small frying pan over medium heat, cook the blueberries, stirring occasionally, until they soften and burst, about 10 minutes. You don't want them to disintegrate entirely, but instead to become a thick blueberry sauce. Transfer the blueberry sauce to a fine-mesh sieve to strain out some of the liquid. You will need 2/3 cup of the thick, berry-containing puree (not the strained puree, which will become your glaze).
Add the flours, sugar, salt, and baking soda to a medium bowl. Whisk until combined.
In a medium bowl, combine the 2/3 cup blueberry sauce, greek yogurt, lemon zest, and egg. Stir thoroughly but gently, since you don't want to destroy the remaining whole blueberries. Stir in the vanilla. Fold in the flour mixture until fully incorporated, then stir in the milk. Spoon the batter into the muffin liners, filling each about 2/3 full.
Bake muffins for 20-25 minutes. While they are baking, whisk together 2 tbsp strained blueberry puree with the confectioner's sugar, until it forms a smooth purple glaze. If the glaze is too thick or too runny, add more blueberry puree or sugar as required.
Let the muffins cool on a rack for 10 minutes. When they are cool, drizzle the glaze on top.