Last autumn, Bill put all his onions sets in the ground on a pocket of proprietory bagged compost (just the usual multi-purpose). The aim was to improve drainage - however, the result was a superb onion crop with no basal rot.
It is possible that keeping the base plate of the onion away from the contaminated soil prevents the disease from getting a grip. Certainly worth a try. The cost of the compost is slight and anyway it will go towards long-term soil-improvement.