I understand your argument, but I disagree that the Marine Times and all the others should stay apolitical to the extent that they have no opinions or leanings on any of the major issues facing our nation, or our military. In order for them to express their opinions in print, they have no choice but to risk the appearance that they are politically motivated. Also, they are private papers and if we truly believe in freedom of the press we cannot put restrictions like the ones you propose on them.
In contrast, base newspapers like the Camp Pendleton Scout are essentially mouthpieces for the base commanding generals and you will never see them disagree with base policies. They strive to be apolitical as they are an extension of the command that should also be also be apolitical. I would argue that our troops need papers like The Marine Times to serve as a voice for issues that base papers will not tackle and local and national papers do not understand. Whether it be body armour, anthrax shots or Rumsfeld, these papers serve an essential purpose and need to have the freedom to report issues in their entirety.
I should also say that I believe they lost some credibility by putting this piece out just before the election. They need the freedom to tackle issues that could be perceived as political, but in order to not risk losing their audience they should be clear that they are not polictically motivated. At this point, demanding that the SecDef resign is a non partison issue.