I kinda like it for some of those smaller conferences that are generally only one or two bid leagues. It makes it more difficult for a middle tier avg team to win the tournament.
And maybe more importantly it gives the top teams more rest. Why not reward the better teams?
Conference tournaments, while fun for fans, are going to start becoming obsolete, especially if (when) they expand the ncaa tournament.
I don't like it, but I understand it, for exactly what you are saying. Reduces the chance of losing your conf champ to an upset.
What I don't like, is it essentially takes the upset fun factor away from fans, and from the players of the lower teams. You gotta win FIVE in a row against increasing degree of difficulty, vs teams that are also rested! To make the dance, that's a tough ticket.
For a Big12 bottom feeder, you have to win 4, but you have a chance to play another upset winner and they played yesterday just like you did. Still a longshot, but at least it isn't nigh impossible.