Drain beans, transfer to a medium pot and add the sage and water. Bring to a boil over high heat, then and reduce heat to low. Simmer, covered, until beans are tender, about 45 to 50 minutes, periodically skimming off any excess foam that may rise to the top. Strain beans and reserve the cooking liquid.
Preheat the oven to 275°. Chop the kale into bite-size pieces. Toss half the kale with 1 tablespoon of the olive oil and a pinch of salt. Place the kale on a baking sheet in the oven and bake for about 20 minutes, until the kale is crisp. Set aside.
Meanwhile, in a large sauté pan over medium heat, heat the remaining 3 tablespoons olive oil. Add the onion and cook until just softened, about 8 minutes. Add the garlic, thyme, lemon zest and red pepper flakes to the pan and cook for 1 minute more. Add beans to the pan, along with four cups of the reserved cooking liquid. Reduce heat to low, and add the butter. Cook, stirring occasionally, until the beans reach a creamy consistency, about 8 minutes. Stir in the remaining kale and simmer until tender, about 3 minutes more. Add lemon juice; if the mixture looks dry, add a bit more of the reserved bean cooking liquid.
Divide the beans among 6 bowls and garnish each with some of the sliced holland chile, some of the grated cheese, a few crispy kale leaves and a drizzle of honey. Serve immediately.