Preheat the oven to 350 degrees. Butter a 9x13-inch shallow ceramic baking dish. In a large skillet, melt the butter. Add the onion and thyme and cook over moderate heat until the onion is softened, about 8 minutes. Remove from the heat. Add the corn and cornmeal and toss to combine. Season with salt and pepper and let cool.
In a large bowl, whisk the eggs with the half-and-half. In a blender or food processor, combine 1 cup of the custard with 1 cup of the corn mixture and puree until smooth. Whisk the puree into the custard. Then stir in the corn mixture, cheese, 2 teaspoons of salt and 1/2 teaspoon of pepper until well blended.
Spread the mixture in the prepared baking dish and bake for about 40 minutes, until the pudding is slightly puffed and just starting to brown. Let stand for 10 minutes before serving. Garnish with crispy bacon bits and chives, if desired.