Lead it and laugh about it. Once the skunk works grows past its initial core, the culture will start to change. It will Make it a crusade. Name the forces of evil you are fighting against. It takes leadership to bring a healthy discipline to a growing organization and at the same time keep its soul intact.
Creative freedom is the essence of a skunk works.
Don't let it get too large. Most important, make it an adventure. Make it a crusade. Name the forces of evil you are fighting against. Revel in your victories.