Atheism is OK
I agree with PZ on all his points. When a scientist looks at any religion, and demands all the same levels of evidence, consistency and cogency from it as he does for anything from physics to biology, he cannot avoid the conclusion that it is a hypothesis on a level with the idea of a 'luminiferous ether' - not only useless but false. Such a person who has come to that conclusion is an atheist by definition. You cannot evaluate religion scientifically without reaching the conclusion that it simply doesn't reflect the real world.
But no one says that as a scientists you have to consider religion scientifically. Scientists do compartmentalise their lives quite well, in that they are still swayed by instinct and emotion and bias in their personal lives. There's no reason that a scientist cannot switch off her logical, curious, enquiring mind to go to church. But you have to understand that this is what she has to do in order to accept religion.
In fact, it is the religious who continue to seek science's stamp of approval, trying to make ideas like creationism seem scientific by inventing Intelligent Design, or trying to explain how Moses could have parted the Red Sea. The only result of focusing the scientific lens onto religion is that you will either show how poor your 'science' is, or you will show how weak your hypothesis is. You are not going to convince anyone but the gullible, and they probably believe you already.
And what's wrong with associating something with atheism anyway? Atheists are moral, secular humanists for the most part, not slavering maniacs ready to tear your throat out at a moment's notice simply because they do not have the ten commandments to tell them not to. According to US prison statistics, you're far more likely to be a criminal if you're religious, so I don't get why the religious seem to think they're better people than atheists. They aren't. Judging by their consideration of religion, atheists are mostly people who see the world in a rational way, who think before they make a leap of faith, who consider an argument on its merits rather than on their own emotional bias, and who believe something when they've seen the evidence. I would much rather have such a person with their finger on the Big Red Button than someone who believes without question that God is on his side and wants him to protect the believers at any cost. I would much rather that person wanted to see evidence of Weapons of Mass Destruction before declaring war, rather than taking it on faith that they would be there.
Theists need to accept the fact that theirs is an illogical choice not supported by evidence, fact, or any relation to the physical world as we know it. And that's okay, as long as you're not trying to pretend otherwise. Many people require the belief that someone is looking out for them, just to get from one day to the next. But many people do not, and if someone is a functional whole person without the need for religion, then the religious shouldn't be offended by that.
To quote PZ:
So, do you believe in Santa?
If we insist on treating people like four-year-olds who mustn't be told that Santa isn't real, what we get is people with the wisdom and attention spans and screwy ideas about how the world works of four-year-olds.