As I understand it, spraying is the best method. You can probably leave affected leaves on, and treat them. Remove any heavily affected leaves, and any fallen leaves to mitigate re-infection.
Small spots can be a sign of stress (under-watering, sudden temperature, swings cold-hot, etc. and are not uncommon, and somewhat normal in the course of the season).
Rust is usually an issue in high humidity locations (such as the South, and greenhouses).