Prep the rhubarb. Cut the rhubarb into thin rounds, about ⅛ inch thick. If the stalks are wide, slice them in half lengthwise first, then cut into pieces.
Make the cream cheese filling. In a small bowl, combine the softened cream cheese, milk, and sugar. Stir and press with a spoon until the mixture is completely smooth and creamy — it may look lumpy at first, just keep mixing. Place in the refrigerator uncovered while you prepare the batter.
Mix the dry ingredients. In a large mixing bowl, whisk together the flour, baking powder, baking soda, orange zest, and salt. Set aside.
Mix the wet ingredients. In a separate bowl, whisk together the oil, both sugars, and sour cream until well combined, about 30–40 seconds. Add the egg, milk, orange juice, and vanilla extract, and whisk until smooth. Stir in the sourdough discard until fully incorporated.
Combine wet and dry. Pour the wet mixture into the dry ingredients and fold together until about halfway combined — a few flour streaks are fine at this stage. Add the rhubarb pieces and continue folding gently just until no dry flour remains. Do not overmix.
Rest the batter. Cover the bowl and let the batter rest while you preheat the oven to 400°F (200°C). This short rest allows the flour to fully absorb the liquid and gives you a better texture. Line every other cup of your muffin tin with paper liners and fill each one nearly to the brim.
Add the cream cheese filling. Remove the cream cheese mixture from the fridge. Scoop a scant tablespoon, shape it slightly in your fingers, and press it into the center of each muffin so it's tucked into the batter. If you like, place a couple of rhubarb slices on top for a beautiful finish.
Bake. Lower the oven temperature to 375°F (190°C) and bake for 17–19 minutes. The muffins are done when a toothpick inserted into the muffin part — not the cream cheese center — comes out clean or with just a crumb or two. Let them cool in the pan before enjoying.