I’ve never seen “Full Metal Jacket”, but Kubrick comes across to me like a guy that mocks/makes fun of, American values and the military, so I’d be surprised if any Kubrick film was actually meant to boost respect for the marines.
I’m not sure the boot camp segment is meant to exalt the Marines, but Ermey’s performance is one for the ages. You really should watch it, and feel safe to turn the movie off when it shifts to Vietnam. It really is a tale of two films, and the second one is not so good.