I think the ending that was done made sense. Think about it: Barring all the "was he killed?" discussion, the ending was meant to convey one thing: Tony can never live a normal life. The constant shots to suspicious-looking people in the restaurant only serves to reinforce that. Even something as innocent as a dinner out with his family, for Tony, turns into a constant game of paranoia - "That guy was looking at me, is he with New York?" or "That guy got up to go to the bathroom, is there a gun there?" or "That guy in the suit.. is he a Fed?" and the like. Anyone could be out to get him, and he can never let his guard down, ever. He can never enjoy being around his family. He can never just enjoy being out somewhere, anywhere, because a black car driving slowly might be a hit, a person following him into a restaurant might be an assassin.

That's what we're meant to take away: That for all his power being the boss of New Jersey, for all his money, for all his desire to care for his family, Tony Soprano has to live a pathetic life of constantly watching over his shoulder, never sure if he's going to live each and every day.

He's damned for the rest of his life due to his own actions and the life he chose. Like Michael tells Vincent in GF3: That's the price you pay for the life you've chosen. For Tony Soprano, that price is to live in fear and paranoia every day for the rest of his life.