Two ways that I know of.
1. Leave the tournament alone, with the winner as a non-database player. Then, create the database player, but NOT by merging the player. This will keep his league points at zero, with no other intervention needed.
2. If you have already merged the player, re-load the tournament, and you can manually adjust the points so that he receives zero points for that tournament.
Between the two, I'd personally suggest the first one.