I was in a similar position in the first game benji where we only had three players playing and one of them bombed early doors. I won it and we only managed to scrape third in the points
The points system is far from perfect as it does encourage laddering up. You could have 4 players finishing in a 30 runner game in places 10th, 9th, 8th and 7th and they would more than likely win the 5 points.
That said, it was sold as a "team" comp and as such we all (well not all, but most it would seem) knew the rules when we entered.
Maybe tweak on the points scoring if there is a next time.