Consider this attempt at a syllogism:
P1: All men have feathers
P2: Socrates has feathers
C: Socrates is a man
We have two false premises and a logical fallacy (affirmation of the consequent) leading to a true conclusion. What should we do about a person who reasons like this? After all, their conclusion is indeed true; any attempt to argue with them might seem to argue for the falsity of their conclusion.
I see something similar arguing against a lot of religious people. Some of the bitterest arguments and outright conflicts I've had are with religious people whose ethics I almost completely agree with. I found the reasoning they used to support their their ethics to be profoundly deficient, and I criticized that reasoning. Inevitably, they drew the conclusion that I was either disagreeing with their ethical beliefs, or that I was being humorless and over-pedantic: why criticize the basis if I agree with the conclusion?
There are some decent arguments for being... ecumenical... about the process so long as the conclusion is correct.
We're all on the same team, are we not? Shouldn't we focus our attention on those who get the conclusion wrong? Why should we give liberal Christians, liberal Muslims, Buddhists, Wiccans, etc. a hard time when they oppose anti-atheist bigotry, when they lobby just as hard (or harder) for what any atheist humanist would call simple human justice and fairness? Shouldn't we work to achieve a good society by whatever means are pragmatic or even expedient? And put our esoteric, abstruse philosophical quibbles away for a more propitious time?
Also: If legal secularism is a virtue (and I do approve of legal secularism), and if law derives from ethics (which I think it does, or should) then should we not embrace secularism as an ethical principle independent of law? After all, I think freedom of speech is a virtue, and while I may be sharply critical of others' beliefs, I have never called for someone to be actually silenced. Shouldn't I then personally embrace secularism as an ethical principle? (The refutation of this argument is outside of the main point of this article; I'll discuss it more in comments.)
As good as these arguments are, I think there are stronger arguments for the contrary position.
Even if you sometimes come to the correct conclusion from a flawed process, there's no guarantee you'll always do so. Indeed, it's highly probable that you'll come to some incorrect conclusions. That's how we distinguish a bad process from a good process. The affirmation of the consequent is not a fallacy because it contradicts some abstract law of logic, it's a fallacy because we know you can use this process to come to a false conclusion. We know the laws of logic are correct precisely because we know from experience that they have never yet led us astray: We have privileged as the "laws of logic" just those particular symbol manipulation rules that we have never seen draw a false conclusion from true premises.
Silence implies consent. If we are silent when someone uses faulty reasoning, then we consent to not only the conclusion, but also to the method used to arrive at that conclusion. What are we to say, then, when the same method is used to arrive at a false conclusion, or an intolerable ethical position? We open ourselves to the legitimate charges of tendentiousness and hypocrisy: that we're challenging the logic only because we disagree with the conclusion. "My reasoning was fine," they might object, "when you agreed with the conclusion; why is it now such a big deal?"
Dealing as we do in imperfect, incomplete knowledge, it is frequently pragmatically justifiable to come to a conclusion that is wrong in some sense for the right reasons, so long as that conclusion is also right in some other sense.
Should O. J. Simpson have been acquitted? From the publicly available evidence (and I have examined the facts presented at the trial) I'm persuaded that Simpson did indeed commit murder. In one sense, the trial came to the "wrong" conclusion. But there's another, larger, sense in which the trial came to the exactly right conclusion: for a person to be punished under the law, the prosecution must make a persuasive case at a trial and convince a jury of the defendant's guilt. The government is not a disinterested party, and one function of the criminal judiciary is to act as a check on the government's power. If we were to permit a compromise of the process to ensure what appears to be a better conclusion in one case, we have abandoned the protection the process gives us in other matters, which may not be so independently persuasive. If we tolerate a kangaroo* court when we agree with its verdict, by what virtue do we condemn a court as kangaroo just because we disagree with its verdict?
In just the same sense, if we tolerate and remain silent when religious people compromise logic and rationality to come to ethical conclusions we agree with, we abandon the protection that logic gives us when they come to conclusions we disagree with. If we tolerate faulty logic when we agree, by what virtue do we condemn logic for being faulty just because we disagree with the conclusion?
There is no doubt that Christianity among black people has had an enormous positive impact on not just the abolition of slavery but for black people's civil rights. And, of course, I completely support total not just complete equality for black people but also active reparations and correction for past injustice and oppression.
But... if we allow "God condemns racism" as a legitimate argument against racism, how are we then to object to "God condemns homosexuality" or "God condemns abortion" as illegitimate arguments? God was good enough for us when we agreed with the ethical conclusion; it looks like we argue against a theological justification only because we disagree with the conclusion, i.e. we're not really against a theological justification per se, just a theological justification we disagree with.
There are some expedient reasons to tolerate faulty logic and unwarranted justifications. If you stop and help me change my tire, I'll be grateful for your assistance, regardless of its source. When some issue comes to a vote, I'll settle for you voting the right way for the wrong reasons. If you want to contribute money to Equality California to defeat Proposition 8 or Planned Parenthood to defeat Proposition 4, I won't ask you why you're writing the check.
But that's as far as I'm willing to to tolerate faulty reasoning for expedience. I will not shy away on the basis of expediency from criticizing religion, even to the extent of criticizing religious people for coming to an agreeable ethical conclusion for the wrong reasons. If some religious people support the teaching of evolution in the school, good for them. I won't stop pointing out that the theory of evolution does indeed dethrone human beings from the center of creation, and if that makes those selfsame religious people uncomfortable, too bad for them.