If you have not already Goggled a search for âÂÂplant rust diseaseâ I would suggest you start there. There is a lot of general information on the web.
You should not need to discard your rhizomes but the fungal pathogens will likely persist in the soil. I do not believe the pathogens will seriously impact the dormant rhizomes. Canna rust typically attacks the foliage. You may choose to over-winter the rhizomes in their pots this winter, but I would definitely discard the soil and wash the containers early next spring before dividing and replanting. Under the right conditions, rust pathogens can easily be air transported from outside sources. Prevention is the main consideration.
You need to consider the cause of the rust in your canna situation; otherwise you may continue to experience the same occurrence in the coming years.
Sanitation and good air circulation for the growing plants should be considered. From your description, I suspect your pots were overcrowded. Potted cannas usually need to be divided each season. Foliage that remains wet in the evening contributes to ideal conditions for canna rust. Only use overhead watering early in the day to allow the foliage to dry. There is not much we can do about prolonged rainy periods but the canna leaves do have a wax like covering that generally aids in preventing prolonged damp foliage; providing there is adequate air circulation.
Hope this may be helpful.

Regards,
Kent