I'm both an atheist and an avid user of and advocate for the National Park Service, so I feel kinda caught in the middle of this debate. The long and short of it, though, is that NPS is being cowardly and disloyal to its mission. However, there are two distinct debates occurring simultaneously, and it's important not to conflate the two.
Debate One: Should the National Park Service permit non-scientific beliefs to influence their educational materials and official statements? Not in a million years! (Or 6,000 years, if that's your game.) If what the Public Employees for Environmental Responsibility say is true, and "Grand Canyon National Park is not permitted to give an official estimate of the geologic age of its principal feature," then I'm outraged. As a governmental entity (and as an organization statedly devoted to education about the natural world), it's legally and ethically wrong for NPS to bow to religion in the face of scientific fact. Boo, National Park System!
Debate Two: Should the National Park Service allow a religious-themed publication to be sold in its bookstore? Sure, why not? As Paul pointed out, there are plenty of books sold in the Grand Canyon bookstore describing the spiritual (and geologically inaccurate) beliefs of American Indians, and permitting Christian creationist texts is no different. The bookstore and giftshop is a clearinghouse for Grand Canyon-themed items, not a library of fact and endorsements. (They also sell Grand Canyon shot glasses in the giftshop. I wouldn't interpret that as a government endorsement to drink.) It's important to note that few, if any, items sold in the bookstore are published or produced by the National Park Service; they are created by private or non-profit groups and sold on NPS property. Insisting that the Grand Canyon bookstore only sell items devoid of religious content is like demanding that public libraries not carry The Holy Bible, lest doing so be interpreted as an endorsement of Christianity. The NPS is permitting a venue in which all voices (no matter how crazy) are heard. Hooray, National Park Service!
If I were to take issue with anything NPS does, I'd complain about their pro-Manifest Destiny video presentation at Mount Rushmore National Monument. Blech.