Keep in mind that Kevin is President of the National Center for Science Education. He isn't speaking for NCSE in this paper but it's fair to say that his view is quite compatible with those of other members of the NCSE leadership.
Here's what Kevin writes under the subtitle "Avoid pitting science against religion, even though sometimes there are real conflicts" ...
... the very openness of science is what attracts scorn from religiousfundamentalists, who build their lives on what they accept as immutable truths of faith. The principal act of faith of a scientist is accepting that the natural world is knowable, and that we can use our (however imperfect) faculties and judgment to learn about natural phenomena and trust our results, wherever our investigations lead. After that, the rules of scientific inquiry are not about faith, but about posing and testing hypotheses. But science has its limits, and the supernatural is one of them. In short, science does not deal with the supernatural. Religion has its limits too, and one of them is in making statements about the natural world. There is only conflict between science and religion if people want it; or rather, there is conflict when people want it. That conflict comes from either side saying more than it reasonably can about its domain. But the non-theistic axiom of science (see below) means that it does not favor or disfavor any particular religious or other supernatural beliefs. In return, its statements about the natural world should not be contradicted on the basis of any sectarian religious beliefs. So, regardless of what some interpretations of old writings about Scripture-professed, scientific evidence affirms that the Earth cannot be 6,000 years old. That is in direct conflict with some religious views. Contemporary evolutionary biologists hold varying religious views; contrast, for example, Gould (2002a), Miller (2007), Coyne (2009), and Asher (2012). But when they operate as scientists, they do not place religious views above empirical evidence.I think there IS a conflict between science and religion. For example, I think that a proper understanding of evolution leads inevitably to the conclusion that there is no purpose or goal in evolution and that the evolution of humans on this planet was largely a chance event. This conflicts with many religious views.
In textbooks, it is appropriate to discuss why evolution or any scientific idea or hypothesis was or is controversial as science (cold fusion is an example). But it is not appropriate to pretend that well-established scientific concepts are controversial. It is also not appropriate to note that some scientific concepts were controversial in the past, without noting the present state of understanding of those concepts (a great many important scientific ideas are controversial when they are first proposed). Cultural and religious controversy about science has no place in science texts, and pedagogical activities that encourage children to have debates about evolution or global warming - in an educational system where they can have only the most rudimentary exposure to these subjects - merely amplify the prejudices of the students’ families.
Is there room to discuss cultural and social controversies over scientific ideas in textbooks? Perhaps, although the focus of a science textbook should be squarely on the science. But textbook authors who choose to discuss cultural and social controversies should be careful to ensure that they are not misrepresenting the science as controversial or offensive to the beliefs of their readers, and thus undercutting the legitimacy of the science.
I think that science can, and has, dealt with supernatural explanations and found them wanting in all cases. I do not believe in non-overlapping Magisteria. There's nothing that science can't investigate.
I believe that Kevin Padian is wrong when he says that religious scientists such as Ken Miller, Michael Behe, and Francis Collins "do not place religious views above empirical evidence." They all believe in miracles, they all believe that humans have a soul, and they all believe in life after death. They all believe in the existence of a personal, creator God in spite of the fact that there's no evidence that such a being exists.
I believe in teaching the controversy. I think it's quite silly to pretend that there's no controversy about evolution when, especially in the USA, huge numbers of people reject evolution. The general public is well aware of attacks on science from Intelligent Design Creationists and Young Earth Creationists. These attacks on science (i.e. controversy) need to be addressed in schools in order to equip students to think critically. Debates and discussions on global warming and evolution in high school are marvelous teaching opportunities. Ignoring the controversy, even if it's religious and cultural, isn't going to make it go away. Ignoring the obvious conflict between science and religion isn't going to make that go away either.
Padian, K. (2013) Correcting some common misrepresentations of
evolution in textbooks and the media. Evolution: Education and Outreach 6:11 (published online June 25, 2013) [doi: 10.1186/1936-6434-6-11]