The hitter is definitely the one out as he is the one who passed the runner. I believe all three of the baserunners are allowed to score and the hit is scored as a single. This type of play has happened multiple times in ML history. As a precedent, on July 4th 1976, Tim McCarver hit an apparent grand slam in Pittsburgh, but passed Garry Maddox between first and second. He was awarded a single with three RBI's. Another example occurred on June 19th, 1974 when Giant Ed Goodson hit a homerun off Bob Gibson but passed the same knucklehead, Garry Maddox between first and second and was awarded a single with one RBI.
One example where it was scored differently was in the 1999 NL Championship Series when Robin Ventura
hit an apparent game winning grand slam in the 15th inning but after each runner had advanced one base, Pratt the runner who had been on first ran back towards Ventura to hug him and Ventura passed him while nobody except the winning run on third bothered to cross home plate. Ventura was awarded a single with one RBI. In the other above cases, the other runners completed their circuit around the basesand were thus counted as RBI's.