I agree the article overplays it. Any organization, be it governmental, corporate or private, would probably do the same. If you want their help and they aren't in the business of movie making, are going to probably refuse it if it casts them in a light they don't like.
Hollywood is fully capable, I'm certain, of providing mock-ups and stand ins for much of what the military provides. I'm sure when it comes to the bottom-line though, this is a much better deal from them.
I just don't see a vast propaganda conspiracy.