Yes, people who are active in the community will tend to wind up with more points. Obviously. That's a horrible downside again because why? Or is there some reason people who write good stories wouldn't also be reading and commenting as well? Reading and writing are literally the only two things to do on this site, and classically they go hand in hand.
One of the main parts of the idea is that you, as a reader and an active member who cares about the community, can flag any story you like. Is there some little gem somewhere you feel is being ignored, or a story that's great but unfortunately just not quite great enough to get in the top 5 where people will actually see it? Awesome, now you can make it more visible and give other people an incentive to read it and discover for themselves how good it is. Maybe they'll even go on to check out the author's other work. Maybe the author will be inspired by the feedback and advice they get to write an even better story, who knows? It's a win-win all around.
Honestly I don't get the resistance this idea is getting - it's not like a people who don't want to bother with it are being punished in any way, it's the exact same system you guys have always had, just with the added option to put a temporary spotlight on a story (whether it's yours or someone else's) and get the author a little extra feedback.