From what I gather from the Serenity director's commentary, the general arc of that season would've been quite a lot like the movie's plot. However, the character of the Operative was created especially for the movie. Quite likely we'd see Niska and Early again.
Another interesting implication of this scenario is what Firefly replaces in the Sci-Fi Channel's schedule. Stargate SG-1 perhaps? If that happened, the sixth season broadcast on the Sci-Fi Channel would've been followed by a theatrical movie Stargate: The Lost City, which would've been fairly similar to the seventh season finale except that the Stargate program would've gone public and they would've actually found Atlantis in Antarctica.
