Yeah, sometimes conservation can be a double-edged sword.
Sometimes I look back on extinct predators that might have regularly hunted prehistoric humans, and I wonder, did they have to go extinct? Sure, they were once all a danger to humanity, and they had to culled for our sakes, but was it worth the ecological damage? I think it all really boils down to your ethics, of whether you do view human wellbeing as more important than animal, or even environmental, wellbeing.
If the Guinea worm went extinct, I’m certain it would have some sort of negative impact on its ecosystem. But should human beings (and our pet dogs) suffer with dracunculiasis, which can make us non-functional for weeks, and even kill us if we’re (very) unlucky enough? Or even playing with hypotheticals here, if the coronavirus was heavily endangered, would it still be ethical to take vaccines? It’s a tough situation to be in, for both humans and the ecosystem involved.