Yes, this doesn't exactly get easy if we are to simply look at it from a typical "pragmatic" point of view. I think the solution to the potential mess boils down to increasing societys focus on rational, practical, philosophy.
If we are to decide what is "human", what is "good for human beings" and "what rights a particular living organism ought to have", then we need to have a much greater emphasis on morality and what morality is even meant for.