So I was asked recently "what was wrong with someone who, because of their religious convictions, chooses not to participate in scientific research (the example used was nuclear bomb research) because of the harm it would give?". When they asked it, it was clear that they thought it was a significant argument for the benefits of religion. At the time, I didn't have the time to go into a lengthy response, so I wanted to put it here.
If someone, out of a genuine concern for the suffering of other individuals, chooses to forgo research which they felt would lead to the needless suffering of those individuals, then I would support it. I could possibly criticize their assessment of the harm (i.e. would this research definitely cause harm, or at least, more harm than good? what is the cost of not pursuing the research? etc...) This is a perfectly secular rationale for the ethical decision, and we could have a discussion, but as long as their motivation was for the genuine well-being of humans (or even animals), then I don't have a problem.
However, if you make the same decision because you felt that the creator of the universe wants you to do it, or you will be punished by the creator if you don't do it, or you will be rewarded by the creator for doing it then I do not support it...it may be the right decision but for the wrong reasons. The problem with making the right decision for the wrong reasons is that you would, next week, make wrong decisions for the same reasons. If you're not held to a legitimate ethical argument, grounded in the well-being of individuals and societies, then you can justify blocking stem cell research and gay marriage for the same "reasons" that you use to direct your own "moral" choices. Further, if you are allowed to simply say "my religion tells me this is true", then that ends all discussion.
Too many people assume that just because it comes from someone's religion then is it correct, or moral, or ethical...it doesn't. We establish the evidence supporting arguments for moral actions through discussion, critical thinking, and the application of reason...towards the betterment of the conditions for all conscious creatures. When faith stands in for a reasoned ethical argument, then the result will at some point lead to seriously unethical decisions.