The "miracles" are not divine but are the work of a Reaper bound by Roy’s wife, Sue Ann, using black magic.
The episode explores themes of faith, fate, and the ethical dilemma of "who deserves to live". Dean feels immense guilt because he was saved while a young jogger died in his place. Scholarly & Analytical Perspectives [S1E12] Faith
Sam takes Dean to a faith healer, Roy Le Grange, who successfully heals him. However, Dean discovers that his recovery came at the cost of another person’s life. The "miracles" are not divine but are the