Germline altering should only be done in extreme circumstances, and I think this is one of them. Even if mosquitoes do pass on vital antibodies (why hasn't this issue already been noticed in wealthy people who have never been bit and have never consumed something that was bit?) or malaria finds a new way to spread or their absence otherwise creates some kind of butterfly effect ecosystem chaos, what's easier to do in 30 years? Artificially re-introducing safer versions of these mosquitoes / mosquito analogs / isolated antibodies back into the ecosystem and finding new treatments for pathogens, or resurrecting the millions of people who needlessly suffered and died of preventable diseases?
And also consider the chance that maybe nothing bad at all will happen if they all die off. Obviously, this is a very risky hypothesis that's nearly impossible to prove or disprove in a lab, but it's just a possibility to keep in mind. Complex systems like ecosystems are fickle. Sometimes removing a tiny piece of a system wrecks the whole thing like a Jenga tower collapsing, and sometimes removing a massive piece has almost no effect at all. Eliminating a parasite species doesn't necessarily mean there will be significant negative consequences. But of course, there absolutely could be.
As long as this technology is tested extremely carefully and applied to smaller real-world ecosystems which can be studied for years before being deployed globally, it seems like the overall best answer is to avoid the short-term death and despair and deal with future problems as they arise.
Evolution by natural selection no longer holds all the cards. Humanity has, and will continue to, supersede it and override it to achieve things that would never otherwise be possible. We don't have to cower in fear of natural processes anymore, because we can intelligently shape our world, and soon other worlds, as we see fit. We still have to understand these systems and processes to prevent externalities, but that doesn't mean we can't cautiously venture into this kind of technology. It would happen sooner or later, so why not right now?
If we do it like the way you are saying I think it will work. At least I think that's the best chance we have. And I totally agree we must take these chances. And And I'm totally on board with the net benefit/ number of lives saves calculus, and also that we must go beyond natural selection to better our species.
We'll probably be okay because people as a whole have a diversity of opinions: some enthusiastic want to push forward, others want to move more cautiously. Put it together, hopefully we get the right balance. I guess this trait itself evolved, from hunter-gatherers. Only tribes that had the right mix of people: adventurers who want to explore new territory and cautioners who want to be careful, survive on average, I think. Hooray for careful progress.