In a small nonaluminum bowl, stir together the onion, vinegar, and sugar. Let stand at room temperature for at least 30 minutes, or cover and refrigerate for up to 1 week.
In a small bowl, stir together the sour cream, lime juice, and jalapeño. Season to taste with salt and pepper. Let the crema stand at room temperature until serving, or cover and refrigerate for up to 3 days.
In a bowl, whisk the eggs with the milk and season with salt and pepper. In a large nonstick frying pan, melt the butter over medium-low heat. Pour in the eggs and cook without stirring for 1 minute. Using a rubber spatula, gently stir the eggs, allowing the uncooked eggs to run to the bottom of the pan, and cook until the eggs are set but still creamy, about 4 minutes.
Fill the tortillas with the scrambled eggs, pinto beans, avocado, cheese, and pickled onions. Drizzle with the crema, sprinkle with cilantro, and serve.