That's a bit difficult to defend in light of the fact that this film and Zero Dark Thirty were demonstrably influenced by the DoD.
When your competing movie has all kinds of bells and whistles, shots of real helicopters and aircraft carriers and all -- and you can't afford to have that because you don't have access to the stuff that the competing movie got for free, this puts you at a disadvantaged position at the box office. Movie production is pretty damn expensive: these days it's not at all surprising to see film production budgets exceed hundreds of millions of dollar (the last Pirate of the Caribbean cost $300 million to make). When movie studios are under the kind of financial pressure that they usually are -- leaving aside advertisement costs, this can actually be a make or break point for them. So, the government is incentivizing the production of a certain kind of movies... and we see the effects of that play out.
A recent Pew research piece revealed that 7% of Americans use Reddit, and the significant majority of that 7% is millennials. If you go to Reddit you probably know they overwhelmingly support Wikileaks (and/or Assange), so the argument that there's no demand for content that challenges America is very weak (whether it be related to the Wikileaks scandal or not). If a high production value movie unabashedly cast Assange as a hero without faults, the movie would be accepted fine by a sizable amount of people, it would make a lot of money: a lot of people see Assange as a mystical hero, they'd shell out money to see that movie.
Another one that comes to mind is the fact that redditers believe it is their God given right to pirate movies.
The day used to be that being negative of Assange at all got you "downvoted into oblivion", but that's no longer the case. People are even able to mention the idea that Assange might have actually did it without having their comment necessarily achieve negative karma.
For example, go read the /r/movies link talking about Benedict Cumberbatch's comments from Fifth Estate about the topics. Assange was certainly positively mentioned, but he had a lot of opposition as well, along with people simply keeping their minds open.
But that's expected I presume. Military owns all those toys (well technically we as a people do but military is the one in charge of them). So if they want to see fit to use them for advertising whatever position they want they can. Most of the time it will be 'Merica Fuck Yeah! position.
Remember one of military's primary PR role is to attract young American men to join it. It is very conscious of marketing. If it also help promote a large goal of justifying war, torture and invasions, I imagine it is a secondary effect.
I don't even know how to possibly "fix" the perceived problem you pose. Make a law to disallow military to give, lend, advertise, promote? Maybe. Or force it to provide equipment, time and expertise to movies it doesn't want to support?