Mepron and malarone are pretty much the same. They both contain the active drug atovaquone. However, malarone also has a small amount of proguanil which is also anti-malarial. Malarone is usually prescribed as 1-2 pills per day which would give you a far lower % of atovaquone compared to the higher dose mepron. Which is usually prescribed as several teaspoons per day. Just one teaspoon has more mg of atovaquone than just two pills of malarone. Malarone is more catered to malaria or babesia prevention such as taking it before you visit a malaria hot spot.
I would go for mepron if your insurance company doesn't complain, it is far more expensive. However, i'd still wait until you are done with the diflucan for now. It would be too complicated for your liver to take so many meds at once. But i'm sure your dr is aware of that.
There are many other antimalarial meds that might also work against babesia if you find your case hard to resolve. I'll list a few. Most of these are not too effective used alone, it usually requires a carefully calculated combination.
Artmenisin or artesunate(herbal extract)