As far as I know if a team is all out, then in the calculation of the net run rate, the entire 50 overs (in this case, 49 overs) are taken, no matter how many overs is used up by the team.
For example if a team is all out for 150 in 35 overs in a 50 over match, then to calculate the NRR, the team scored is divided by 50. (The RR of the opposition is subtracted from the RR of the team to get the NRR.)
Also unlike the SA vs AUS 1999 WC semifinal which was a Knockout game, this one is a group game, and hence in case of a tied score, 3 points must be awarded to both teams. (Which means NZ should play the final in place of England:crying )