If you are going to abolish the conferences then you will also need to balance the schedules, otherwise you are just giving free passes to Miami and Indiana to get the top 2 seeds in the playoffs. If there was something inherently unfair in the current system then I would say intervene, but much like Duncan's early season shooting woes, what we are witnessing is just a slump and eventually the performance of the conferences will revert to their mean in the coming seasons.
The problem with balanced schedules is that East Coast and West Coast road teams will have more odd tip off times for their home TV audiences. A 7:30 tip in Atlanta is 4:30 in Portland. A 7:30 tip in Sacramento is 10:30 in Indianapolis. It is not fair to the fans in those cities who want to enjoy their team's road games to force them to watch more bad tip off times to fix something that isn't really a problem.
In fact, I don't see this as a problem at all. The Western Conference playoff race is going to be fun to watch...especially from our perch on the top of the pile. Embrace the extra competition because as I said, it won't be like this forever.