I like the points system the way it is, though I am kind of intrigued by the suggestion of negative points (which I kind of flirted with in this league anyway

.) I also agree that the frequency of the tourney is not good (too many games!), and weekends would work out better for me. Maybe having two events at the same time, but one on Saturday (buy-in) and one on Sunday (freeroll)?
People will still have conflicts (I can see that I would have occasional Sunday conflicts already), but if the final tourney game allowed double points, as someone suggested, that might give people a chance to place.