To me, this sort of violent act, while not okay, can at least be forgiven. It is up to us to protect other living things. And many of us have the idea that we're superior to other creatures, but who are we? It's immoral to believe we should be treated more fairly.
Violence ins't the answer for anything you can't use violence to stop violence. There are better courses of action than these methods. If you go to jail how do you expect to save more? I think you would do better by being outside the walls in order to save more creatures.
No, a violent act from a private citizen to save the lives of a disappearing species is not grounds for forgiveness in the legal system, because that is not the definition of a necessity defense. A person can only claim necessity if the harm that they are avoiding is worse than the harm that they are perpetrating.
If someone commits a violent act, that was not self defense or defense of another person, they should be punished accordingly. While disappearing species are a tragedy, they are not an excuse to go out and assault someone. The best way to save the lives of disappearing species is to lobby for stronger laws.