CLB - I like that interpretation of the extended refit a lot, and it certainly explains away a great many of the visual changes between WNMHGB and TCB.
The more militaristic mission also ties into Kirk's original monologue:
Enterprise Log: Captain James Kirk commanding. We are leaving that vast cloud of stars and planets which we call our galaxy. Behind us: Earth, Mars, Venus, even our sun are specks of dust. A question: what is out there in the black void beyond? Until now our mission has been that of space law regulation, contact with Earth colonies and investigation of alien life. But now, a new task; a probe out into where no man has gone before.