This is necessarily a value judgment, isn't it? There are tools like lifecycle analyses and environmental impact reports and threatened species lists that can help estimate/enumerate impacts. But ultimately how much to care is a personal question, and people are going to disagree over whether some small fish or rare owl or fluffy panda is worth more or less than someone's job or a local industry or just some other charismatic species.

Species will always come and go, and they're going to die off faster than we can protect them, sadly. We only get to decide which ones to prioritize, at different personal, local, national, global levels etc.