The way I've always seen the "Navy Vs Marines" situation is this:
WHENEVER Oda actually uses other languages for things, he actually puts the other languages in the dialog, as either Katakana or Furigana.
Example: ALL Of Sanji's attacks are written out in French in the Furigana. Robin's "Seis Fleur" is written in French and Spanish in the Dialog, IE when you hear the Voice actress read off, she doesn't read it off as "Roku Hana" she reads it off as "Seis Fleur". When Luffy calls out Gum Gum Pistol, he doesn't shout "Gomu Gomu no Juu (Pistol)" He calls out "Gomu Gomu no Pisutoru!"
When they say "Navy" they say "Kaigun". The dialog never says "Marine", it says "Kaigun". The only time Oda has EVER written "Marine" in the dialog is for "Marineford". So you can't say "Oda meant Marine" because if he did, why didn't he write it that way?
It's easiest to take this the way FUNi seems to be taking it. The organization is the Navy and the grunts are the Naval Marines, which is why you only really see "Marine" on the grunts and the ships, while at HQ it's only ever written "Kaigun" in Kanji.