The ending as filmed does make sense, but it's a lot subtler than the original script. After the “human” Patrick McGoohan, or Drake if you like, symbolically “dies” and descends through the morgue, he comes out in a lush, private room where the only other person that matters is Number 2. This is a metaphor for the Village. The party-goers now represent the “real world” and the fact that they have sentenced him to death is of no import in that room, where, from the perspective of the one-way mirror, he's already gone, never to be seen again. (just as they've “killed” him to the real real world with the body released in his guise) Of course, the death sentence is play acting, but it's the very same play acting the would have led to a murderous mob in the moment, with a subtle second message for No. 6 — The real world is more dangerous for you than this place. Of course, the death sentence pronounced onto him symbolically underscores the fact that he is dead to the real world, and he'd be better off forgetting about the outside and accepting his new life.

When Number 2 talks about the “initiative he's shown”, she's referring not to his escape from the morgue room, but to the reason that he's wound up in The Village in the first place, a celebration of his lifelong accomplishments. At the same time, she's admonishing him one final time to let it go and be happy in his new life. Her goal is to make him resigned and complacent there, so that they'll have a better chance of slipping him up.

He refuses, but only through sheer force of his determined will, which signals the end for this “kinder and gentler” Number 2. Her implementation is spot-on and 100% successful as far as her plan is concerned, and yet he refuses to give in.