Heat oven to 300 degrees. Butter baking dish large enough to fit beets in single layer.
Scrub beets and trim tops to 1 inch. Place beets in prepared dish and cover. Bake until tender when pierced with fork, about 1 hour. Transfer to colander and cool briefly under cold running water. When cool enough to handle, slip off skins. Slice 1/4" thick (about 3-1/2 cups).
Heat 2 T. butter in large heavy skillet over medium-high heat. Add onion and saute until somewhat tender but not browned, 2-3 minutes. Remove from skillet.
Combine remaining 2 T. butter, the syrup, orange juice, mustard, orange zest, and pepper in same skillet. Heat over medium heat to boiling. Add beets and onions; cook, turning frequently with spatula, until syrup is absorbed and vegetables are glazed, about 4 minutes. Serve at once.