One of the takeaways of the article for me was that it's a small subset of all mosquito species that are conveying this disease. I'm not an ecologist, but wouldn't the elimination of one sort of (disease vector) mosquito lead to a different (non-disease vector) species taking over the niche in the ecosystem?

Some other mosquitos would likely take over the "human" niche yes

But if the Malaria parasite is gone they may not be infected. If it's not gone the parasite would eventually adapt to the new mosquitos.

The article is only talks about killing off a small subset of all mosquito species.