Humans (and our ancestors) have been processing food for at least 1.8 million years. Roasting, drying, grinding, and other techniques made food more nutritious, durable, and tasty. This helped our ancestors to colonize diverse habitats, and develop settlements and civilizations.
Many traditional foods used in cooking today are processed in some way, such as grains, cheeses, dried fish, and fermented vegetables. The processing itself is not the problem.