This is really a question of how much of the rights of a human do we give animals? Giving them no rights doesn't make sense from an ethical perspective as they have sentience and the capacity to feel pain. And yet we don't grant them the right not to be confined or killed, not just because it would make meat-eating humans unhappy, but also because rights are a human concept, and animals in nature are so horribly brutal that it seems incongruous to try and make humans not confine or kill them.
If simply concerned about wild species going extinct, and not their their occasional mistreatment (which is discussed above), species will be conserved by the free market to the extent that there is interest in them and the ecosystems that they support, eg., in zoos, wildlife tourism, forest products, etc.
If your pollution damages the property of others, that would violate the NAP, and a minarchy would be justified in collecting penalties for the same and distributing them to the people affected. This should incentivize the company to try and prevent or clean up its pollution as much as possible. We need to decide the extent of such penalties, and whether penalties other than monetary ones would be even more effective at preventing pollution.
