Yep, and in fact it was the norm not to prosecute leaks for many years, whether pro Administration or anti Administration leaks. The realities of power meant that there were more pro Administration leaks, but at long as there were no prosecutions it was acceptable overall. However, there were always those especially in the DOJ who wanted to stop leaks.
Ironically, it was the outrage and push for leak prosecutions in the Valarie Plame affair under George W Bush that led to the current situation. Yes, those were pro Administration and pro war leaks, and I understand that people feel that prosecuting pro Administration leaks is "punching up" unlike the "punching down" against Manning et al. (I also realize that the investigation didn't lead to an Espionage Act charge itself, but a charge of lying to investigators - but they were looking to make Espionage Act charges except that the lying frustrated their investigation.) Plame and Scooter Libby set a precedent which led to all the current leak charges under Obama. The reason why Obama's Administration has prosecuted more Espionage cases for leaks than all others combined isn't because there are more leaks, but because of the precedent set at the end of Bush's administration - a precedent initially cheered by those seeking to stop war and preserve civil liberties, never thinking about how it would be turned against themselves.
That is, sadly, the reality of power politics. The fairness norm and equality is really strong, as is precedent. A legal theory doesn't stop at "punching up;" it will be used against the less powerful as much and probably more so than against the powerful. So a lot of a antiwar and pro civil liberties folks were unfortunately sowing the seeds of our own problem.