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I believe maximizing the utility of human lives is the most important thing if we are to speak from a consequentualist perspective. For that matter utility might be minimized if the planned extinction of a species were to take place or it might be maximized. To separate human beings from nature is a fallacy in my opinion. We are just as natural as anything else, and the extermination of dangerous species fits quite fine with the Darwinian view of survival. It is just a long-term, planned survival - which is what our intelligence is good for.

So no I don't think it is wrong ethically to kill off bacterial diseases or even mosquitoes if it will save many human lives or the lives of other more valued species. Sure it might lead to unforeseen consequences, particularly in the latter case, but this is true for any activity any individual makes in any situation. There is a calculation problem in how this might affect the environment otherwise, and if negative effects are so debilitating a portion of the population would preserve such things through spontaneous action, not planning.