Preheat oven to 400 degrees.
Trim greens from beets, reserving stems and greens. Place beets in baking pan, cover with foil and roast until very tender when pierced with a knife, 45 minutes to 11/2 hours, depending on size of beets. Uncover and let cool Reduce oven to 350 degrees.
While beets cool, arrange baguette slices in a single layer on a large baking sheet. Bake, turning slices over once halfway through, until toasted but not browned, about 14 minutes.
Thinly slice beet green stems and finely chop leaves; keep stems and leaves separate. Heat 1 tablespoon oil in a large skillet over medium heat. Add stems and cook, stirring occasionally, until tender, about 3 minutes.
Add remaining 1 tablespoon oil and garlic and cook, stirring, until fragrant, about 15 seconds. Add greens, vinegar and water and cook, stirring occasionally until greens are tender and liquid has evaporated, 4 to 5 minutes. Stir in salt and remove from heat.
Peel cooled beets and cut into 1-inch pieces. Place3/4 cup beet pieces, goat cheese and pepper in food processor and purée until smooth (reserve remaining beets for another use).