I'm not sure I understand what you mean. I agree enthusiastically that taking your morals from the dead scripture of an old religion is a terrible idea. I also think that we should try to make all of our decisions as rationally as we can.

But I also think that there are certain questions that I answer irrationally, but with great certainty. The best example I can think of is torture. (Sorry to be gruesome.) When I think about whether the torture is justified, my immediate answer is no. I am not certain, but I don't think a rational argument could convince me otherwise. I could probably be convinced that mild forms aren't always bad, but the more extreme stuff-- no way.

I think my position could be summarized as "There is a subset of decisions that I can't make rationally, even though I think it would be better if I could."