There is certain anti-malarial medication which is not acceptable (e.g. Lariam), but Malarone is not one of them, at least for the FAA:
Anti-Malarial - The following medications are acceptable for malaria prophylaxis:- Chloroquine Phosphate
- Malarone (Atovaquone + Proguanil HCL)
I don't know about Europe, but I guess it should be the same.