I think it may be better to reset the terms we are using because, technically speaking, all seeding rules are manipulating the seeding order. I think it would be more accurate to say that we're discussing the fairness of the seeding rules in light of the evolution of the super conferences which makes it harder and harder to avoid conference foes.
Maybe we don't throw out the rule but tweak it. For example, we change the rule to only allow rearranging to prevent conference teams which have played 2 or more times during the regular season and conference tournament. This season, that would still prevent South Carolina from being paired with Texas, LSU, Kentucky or Alabama but not from being paired with any other SEC team in the tourney (Ole Miss, Vanderbilt, Oklahoma, Tennessee, and Georgia). I think that would keep the spirit of the rule while giving the committee some more flexibility to pair conference teams that only played each other one time.