Update: Military.com notes:

a week after the Military Association of Atheists and Freethinkers submitted the petition on WhiteHouse.gov the effort has garnered just 25 of the 25,000 signatures it needs by Feb. 5 to get any kind of response from the White House.

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Jason Torpy, a former Army captain and current atheist, has filed a petition on WhiteHouse.gov to have “no religious preference,” or “NO REL PREF,” removed from the options in troops’ military records. He also wants the question removed from the list of requirements during inprocessing, making it an optional “opt in” later.

The latter is probably extremely unlikely.  First, the military has been mandated by law to make a variety of things a “mandatory opt in,” based on the belief most servicemembers will never make the extra effort to do so otherwise. (For example, one congressman floated the idea of forcing members of the military to enroll in the pseudo-retirement “Thrift Savings Plan.”)  Torpy explicitly stated there was pressure to “choose Christianity” in basic training: 

Torpy told CP that the religion question on the forms puts pressure on new recruits to choose Christianity. He said this stems from “the well-known religious nature of the military and of the United States, as well as the institutional pressure to conform to the majority.”

He cites no evidence of institutional military pressure to choose Christianity, nor does he explain how so many new recruits are able to withstand the pressure and select the religious preference they actually prefer.

Second, the US military lives and breathes metrics and demographics on everything from race to hometown to level of education.  Even Torpy has defended the use of religious demographics:

Religious demographics are kept as a standard piece of information.  And as a matter of fact, our organization has no problem with that because it helps chaplains to foster both religious freedom and religious accommodation…when the information is used appropriately.

(That his suggestion would undermine his own defense seems to escape him.)  In fact, such demographics are so ubiquitous it was a mini-scandal on both sides of the aisle when the Department of Defense said it would not track sexual preference after the repeal of “Don’t Ask, Don’t Tell.”  Demographics on religion are used for everything from deploying Jewish Chaplains to the war zone during Hanukkah to helping chaplains know how many services to hold and what type.

As to the first question, there may be some validity to Torpy’s request, as “NO REL PREF” could be perceived as confusing.  Torpy’s solution, however, is no less confusing:  Replace it with a “blank.”  That doesn’t really solve anything.  Torpy’s justification is somewhat strained:

Torpy said the problem with having a “no religious preference” option “implies any individual would be ok with any religious practice or faith tradition, whether it’s Wiccan, Buddhist, or Protestant. That is an unreasonable assumption to make because people generally have very strong beliefs about their religious preference, even if that preference is no religion at all.”

He’s right:  That’s an unreasonable assumption, but there’s no evidence anyone but him has made it.  The “implication” he cites may be true in Torpy’s mind, but there is no factual reason to believe the US military thinks “no religious preference” is equal to “any religion.”  Nor does Torpy explain how “blank” would fail to create an identical problem to leaving the system as is.  Finally, if there is pressure for new recruits to choose Christianity, as Torpy has said, why is “NO REL PREF” a problem?  Torpy can’t have it both ways.

In truth, the “NO REL PREF” option was probably the best someone could come up with at the time.  Contrary to Torpy’s implication, the US military is loath to leave anything blank due to the assumption the absence of data is an administrative error of omission.  For example, in many military manuals blank pages contain the text “This page intentionally left blank” or even simply “(blank)”, (which always begs the question, is the page then really blank?).  NO REL PREF has led to confusion in the past, and it may have obscured some demographics.  Of course, some choose it intentionally to obscure their own demographic.

Torpy’s petition truly seeks to make a mountain out of a molehill, but he may have other motivations.  He once claimed that “NO REL PREF” was the hiding-ground for non-theists in the military, and he used NO REL PREF numbers to inflate the statistics of atheists in the military by a factor of 50.  He was taken to task at the time, but defended himself by making the ironic moral judgement that

It is fair to conclude that those in majority faith categories (ie, Christian) with any measurable faith would choose their specific denomination.

Trust an atheist to judge the level of devotion of people of faith.  Regardless, by removing “NO REL PREF” and creating an awkward and even more confusing “spiritual but not religious,” Torpy may be surreptitiously trying to force atheists in the military to declare themselves, potentially increasing his visibility.

The US military does have a need to maintain some form of demographics on the religious preferences of its troops, because it needs to know how best to equip itself to protect their religious freedom.  How it chooses to administratively manage those demographics is its own prerogative, despite Torpy’s interesting, if fairly insubstantial, “suggestion.”