I mean, you're complaining about a (THEORETICAL) agenda being pushed in the sequel to what is very likely the GREATEST propaganda movie of all time...
I wouldn't go that far.
This film didn't even have a real enemy.
It was a rock video based around real life with the required Hollywood nonsense sprinkled in. It (thankfully) painted the military in a much-deserved positive light after decades of post-Vietnam doldrums.
You were probably not even alive then. America was finding her confidence again. The economy was booming after the malaise of the disastrous 70s. The military was being revitalized. It was okay to be a patriot and wave the flag. This movie just happened to come along at the exact right moment.
The Navy had script review authority in exchange for cooperation but it wasn't their project and it was not misleading. Propaganda? No.