The key is to take effective doses of antifungals which don't simultaneously wipeout the good bacteria. For this, I believe caprylic acid / coconut oil are the best. These kill off some gut flora, but a majority of the good guys remain unharmed.
Large doses of Grapefruit-Seed-Extract and oregano oil will kill off the good gut flora. Oregano oil would be an awesome antifungal but for the destruction of friendly bacteria. In theory, large doses of probiotics could replenish the gut flora which oregano oil destroys ... but who knows how much will be needed ...
Garlic is also an awesome antifungal, and you will find countless Internet articles that claim that garlic will leave the good bacteria UNHARMED. However, this is pure conjecture (unsupported by scientific testing), and I don't believe it to be accurate. Thus, garlic is an unknown.