This is a fantastic and very complicated/nuanced question. You've touched on the fact that conservation, in the end, is a value judgement - based in what people want to prioritize. As far as coyotes, I think we still have a ways to go as far as assessing whether they are negatively impacting listed species in their new eastern ranges (as compared to the impacts of other non-native species like outdoor domestic cats). The other challenge with an animal like the coyote is that the slim evidence we have shows that lethal control (if a wildlife manager was into trying that) wouldn't work, and their populations would quickly rebound. Thus, I imagine this will have to be a very context-specific answer, where we create solutions on an individual-species basis for our endangered and threatened species, while simultaneously increasing our empirical understanding of whether and how expanding mesocarnivore populations are impacting species of interest. Not a satisfying or clear cut answer, I'm afraid, but nothing in conservation ever is!