well you could say this about any behavior. Why teach children to stop peeing their pants, isn't that just trying to force them out of their nature?
There's nothing abusive about training a dog about proper behavior. Anyway, I think a dog's nature is more about obeying humans than digging holes. That's kind of the deal we made thousand of years ago
peeing their pants will make them smell and mprobably irritate the skin. digging holes is a completely normal behavior for a dog (unless it's excessive or coupled with abnormal behavior).