Bring water to a boil in a large saucepan, then add 2 tablespoons salt. Add onions, and cook until just tender, about 12 minutes. Drain. When cool enough to handle, trim root ends with a paring knife, and pop onions out of their skins. Let dry on a paper-towel-lined baking sheet.
Melt butter in a small saucepan over medium heat. Add flour, and whisk until mixture bubbles slightly but has not started to brown, about 1 1/2 minutes. Slowly whisk in milk. Raise heat to medium-high, and bring to a boil, whisking frequently. Stir in remaining 3/4 tablespoon salt, the nutmeg, and sage. Reduce heat to low, and cook, stirring occasionally, until thickened, 12 to 15 minutes.
Stir in onions, and cook over low heat until heated through, 5 to 10 minutes. Discard sage, retaining a few leaves for garnish if desired.