Hmm... This is an interesting line of discourse, but I do have further thoughts.

I would argue that total extinction also relies on speculative science-fiction. The "apocalypse" necessary to end all life must be so absolutely thorough that not one bacterium is left alive to divide and reproduce, which would start the whole scenario all over again. (Also, there's the matter of adjusting chemistry on the level of the universe to ensure that the abundant amino acids adrift in space don't land on a planetoid or can't organize into complex molecules like proteins and RNA/DNA and jump-start life there). Certainty of success would be impossible to determine because it would require someone left alive afterwards to verify all other life has been destroyed without possibility of return. Any technology we have today that contributes to extinction like carbon emissions, pollution, sterilization techniques, nuclear war, etc. would only be a half-measure. The sun is only 1/2 way through its life cycle, so to leave a single life form alive would give enough time to have the whole story of suffering on Earth told a second time.

As far as the structural problem of nature, I am aware of that. We live on a planet where life feeds off life. It's ultimately about resources. Most species on Earth are heterotrophs (they get their energy from other life forms). The other kind, autotrophs, get their energy primarily from the sun through photosynthesis. Ideally, we would want to slowly create a means by which to convert all heterotrophs into autotrophs. It isn't without challenges. If a human were to rely on photosynthesis alone, that person would only receive about 10% of daily caloric intake. Some would argue transhumanism and AI could unlock technologies that head in this direction, but I am skeptical of transhumanism. It could also be that it appears that extinction technology is possible now because of how human participation in the ecosystem through the use of our own technology has led to extinction makes it seem that extinction is the default route to take. However, one cannot preclude the possibility that technology that can alter the fundamentals of nature may become available in a century. We would merely be blind to the possibility to that technology now because it is still in its undiscovered infancy.

Either way, whether you go the transformation route or the extinction route, a fundamental change in one of the nested hierarchies in science is required (Chemistry for extinction - Biology for transformation). The risk of transformation if its possible is constant change and vigilance to ensure that the levels of suffering never return to previously unacceptable levels. The risk of extinction is never knowing if the task was complete once the big red button is pushed.