There are people who sincerely believe "meat is murder." In other words, that killing an animal capable of experiencing terror and pain is wrong in the same way that killing a human being is wrong (though perhaps different in degree, or not). There are other people who, while willing to eat meat, find the conditions that animals live in before they are killed deplorable and would prefer to eat the flesh of an animal that at least gets to experience a more dignified existence before its death.
Now, because the first group advocates a more restrictive standard and takes issue with the second groups willingness to eat meat, is the first group responsible for undue suffering of animals because they fail to acknowledge the reality that people will continue to eat meat?
Yes, this analogy is very inexact in comparison to the positions of monogamy vs. condom use in preventing AIDS. But the general principle is that someone advocating a higher standard is not responsible for others failing to live up to a lesser standard. So, if the Catholic Church advocates monogamy, that does not make them responsible for people not at least using condoms failing that. The only argument left is that the Catholic Church should make gradations in their arguments (condoms bad compared to monogamy, but not as bad as non-monogamous unprotected sex).
(Not a direct response to the article, but to other comments spread throughout this thread. Instead of picking just one to attach this comment to, I'm putting it at the top level.)