Nick's statement that Gatsby "turned out all right in the end" certainly does seem odd and is ironic given the fact that Gatsby ends up dead at the end of the novel. We might expect that someone who "turned out all right" was alive and content, though maybe not living his ideal life. Instead, Gatsby has been gunned down by Myrtle's husband, George, after Gatsby takes the blame for running Myrtle over with the car (Daisy was driving and Gatsby covers for her to protect her). Gatsby is not only killed, but the novel suggests that Gatsby's attempt to play the knight to Daisy's damsel in distress yields nothing really positive; it only allows Daisy and Tom Buchanan, already irresponsible and frivolous people, to escape with no consequences and thus continue to live their irresponsible and frivolous lives.
Nick's statement, then, better reflects Nick's attitude toward Gatsby than anything literal or factual about how Gatsby's life "turned out." Nick favors Gatsby over the other upper class characters (namely, Daisy, Tom, and Jordan), even saying at one point, “'They’re a rotten crowd' ... 'You’re worth the whole damn bunch put together.'" Nick seems to admire Gatsby's devotion to his ideal, represented by Daisy herself. Gatsby knows what he wants, and everything he does in his adult life is a means to that end. Nick seems capable of ignoring the shadier elements of Gatsby's character, like the questionable way he has earned his money and his vague background, and focusing only on what he sees as the positive parts of Gatsby's character. However, in the same chapter of the novel in which Nick says Gatsby is "worth the whole damn bunch put together," Nick also says to the reader, "I’ve always been glad I said that. It was the only compliment I ever gave him, because I disapproved of him from beginning to end." This comment reflects an inherent ambiguity in Nick's perspective toward Gatsby, but even if he is critical of Gatsby, Nick holds him as better than those other characters of the "rotten crowd." So relatively speaking, even if Gatsby is no longer living, Nick sees Gatsby as superior to the Buchanans and Jordan, which could make Nick see him as "all right in the end."