I read the article and although the reasons listed are valid, this plan just wouldn't work. The mechanics of trying to figure out which teams are going to be in which division, and figuring this out on a yearly basis would be too complicated. It would pretty much water down the concept of even having divisions.
Baseball does a pretty good job of having divisions that are aligned based on either historical or geographical rivalries, and having teams switch due to competetive imbalance doesn't seem to be the answer. The real solution of course would be to change the overall financial landscape of baseball, i.e. salary cap, and you know that isn't likely to happen for a while.