Consider what happens if BYU joins the Big 12 and the Big 12 dissolves. Where does BYU put its non-football sports then? The WCC? Not bloody likely. The MWC? Zero chance. The WAC? That's about the only hope left. Nothing else fits geographically. The Pac 12 certainly aint interested. If BYU burns a bridge with the WCC, it may really bite them in the end.
Of course, on the flip side, if BYU spurns the Big 12, what are the odds they ever join a major conference? Almost zero. They are putting all eggs in the "independence formula will succeed" basket. The Big 12 certainly isn't likely to take them ever again and we know where the Pac 12 sits. Turning the Big 12 down is not without risk.
Just a note to those of you who think this is a no-brainer. These issues involve extremely complex decision trees, and many of those trees end in disaster. I'm confident the data Holmoe and crew are working with, however, is far superior to the data we have here. Give them some credit. They got us this far, and where we are today is pretty darned fantastic.