Bacillus are well studied, mostly benign, soil microbes that produce multiple compounds that prevent fungal spores from germinating and can even directly prevent fungal growth. In the soil environment this allows the bacilli to utilize precious nutrients needed for growth and gives them a competitive advantage over other organisms.
When it comes to the coffee plants, we are dealing with a fungus that lives on leaves rather than soils. The challenge is getting the spores and associated biochemicals on the leaf. Can the Bacillus be cultured in a liquid broth at the farm level to encourage biosurfactant (strong antifungal compound) and then sprayed frequently on the coffee leaves following rain (spores require high moisture levels to infect the plant). Also, could a binding agent be added with the bacteria to help them remain on the leaf for longer term protection.
While breeders are working on more rust-resistant plants and using quarantines, I think investigation natural microbial solutions can help minimize damage from rust and other fungal cultures.