The most important thing to recognize here is that bananas used as crops do not exhibit genetic drift (they are sterile). We clone new bananas from existing plants. Many of the bananas today, including the Cavendish, are thus very vulnerable to diseases like the fungus mentioned.

Genetic modification is one of the few ways we can keep the bananas we like while adjusting them for more recent diseases and pests. The only other way I know is to go back and find the ancestral species, and try to breed a fertile banana cousin.