Here’s the best brief explanation I’ve come across of what lies behind the battles at Baylor. A taste:

The Baylor conflict has pitted "moderate" Baptists against this diverse national coalition -- call it the ecumenical traditionalists. Are they conservatives? Yes, mostly. Are they in favor of "Christian education"? Yes, in the historic sense of the term. Are they "fundamentalists"? No, they are not. Many of the central thinkers in Baylor’s move toward the integration of faith, research and learning are Roman Catholics and mainline Protestants.

What puts the moderate Baptists at odds with the "mere Christians" represented by Sloan is the issue of "soul competency," which implies the encounter with Scripture is intensely personal, and not creedal or doctrinal. On this view, Baylor’s Baptist character is expressed extracurricularly or in religion classes. The content of the particular disciplines derives from the disciplines themselves, not from any particular Christian intellectual encounter with them. Sloan clearly challenged this view, insisting that a distinctively (albeit merely) Christian tradition inform the disciplinary self-understanding at Baylor. This isn’t fundamentalist by any stretch of the imagination, having more in common with, say, the folks at Touchstone Magazine.

Terry Mattingly, who authored the post I quoted above, says that this is the most illuminating piece that he has read about the controversy at Baylor.

For further illumination, from a point of view more sympathetic to critics of the Baylor 2012 vision, go here, here, and here. These thoughtful defenders of Baylor’s traditions cast themselves as members of a particularistic community (warts and all) against a kind of abstract "Northern" and hence alien universalism.

So the Baylor battle is between two kinds of "conservatives," those who would preserve the Baylor of old, a decent regional institution that moderate Baptists "saved from the clutches of the fundamentalists," and those who would use Baylor as a vehicle--a "protestant Notre Dame"--to preserve a distinctively Christian intellectual tradition against the secularizing forces of the academy. Old Baylor couldn’t do that, but tried rather to combine Baptist piety with conventional academics. Perhaps a highly personal Baptist piety could survive that encounter, especially if the academics are both conventional and only moderately good, but it’s hard to imagine that the mix wouldn’t ultimately favor the element that had the greater intellectual force. From the outside--and I am very much the outsider--it looks to me that the Old Baylor was headed down a track toward becoming increasingly conventional and increasingly secular.