I have had malaria of various types and in varying degrees of severity more times in my life than I care to count.
The Vivax strain of malaria can be recurring in some people, but before you become feverish, you feel so crappy that you shouldn't fly - remember pre-flight checks include your health and fitness. So long as you don't have malaria at the time and are fully recovered from exhaustion that follows any fever type disease, there is no reason why you can't fly.