To be fair, most of them would have gone extinct anyway. And besides, we are a part of nature anyway, so why should we feel bad, or even responsible, of the extinctions that took place before we gained an awareness of our potential power to influence other lifeforms, as well as an inherent sense of morality towards their preservation?
Also, we are deliberately making species such as smallpox, tuberculosis and other diseases extinct, and noone will condemn that line of thinking.