The previous magic bullet against Malaria was called Dichlorodiphenyltrichloroethane, commonly known as DDT.
DDT worked very well, initially, but its effects and consequences were intractable and long-term. It's still deployed to various degrees of effectiveness, but usage is far more complex than the initial promise of getting rid of Malaria.
A GM fungus 99% kill rate sounds good, but for insect populations that might not be enough. You likely can't use it again to kill 99% of the 1% left, and so on.
DDT is a chemical. You can stop using it to mitigate some of the unforeseen side effects. How can one retrieve or stop GM fungi in the wild? What patterns of resistance will emerge?
With DDT we got "lucky". It turned out to be overall effective when combined with guidelines and different approaches, but it never rooted out malaria completely by itself in one fell swoop.
Creating natural enemies of a pest by genetic modification is a valid approach, but not something to deploy wide-scale at the first hint of success.
https://en.wikipedia.org/wiki/DDT#Malaria_control