I'd much prefer the (theoretical) gene drive.

Bad outcomes for gene drive are either that it doesn't work, or the mosquitoes go extinct in nature and cause more ecological issues by their absence. The worst problem is fixable by keeping live specimens for reintroduction. In fact, since malaria is the target and not the mosquitoes, reintroduction might be a good idea after malaria becomes extinct.

Bad outcomes for the fungus is it becoming uncontrollable and starts killing other insects. Reintroduction becomes impossible without engineering a new, immune mosquito. Or that evolution backfires on the spider and causes them to go extinct. Or all of those happening together.

Comparing the two, the fungus has all the downsides and more, with zero upside.