Reading Dr Davis' article in the 9Mark ejournal, it sounds like he did exactly what the scripture outlines for organization of the church's spiritual and servant leadership. Most Baptists look at elder rule as being a "Calvinist" influence, and perhaps that's so, but if you look at the role of "Deacons" as described and recorded in scripture, they were never intended to serve as a "board of directors" or on a level of spiritual authority accorded to the congregation as a whole and to the pastor as the "overseer". Paul and Peter both define the positions, indicating that the pastor is the "head elder" and the work of the elders extends to providing spiritual leadership in preaching, teaching and ministry of the word, while the deacons are the church's servants. Most Baptist critics of this way of doing things appeal to "traditional Baptist polity" rather than submitting to a "presbyterian" form of church government, but actually, in this particular case, as Davis describes it, the elders function under the authority of the congregation.
His description of the church leadership when he arrived, with a group of deacons who exercised power and control because of who they were, what they contributed, and how long they had been there, could have applied to thousands of Baptist churches anywhere. It is certainly similar to several churches in which I have served. Nine times out of ten, they are not interested in anything except maintaining the status quo of the church, control of the budget, and are committed to keeping the pastor "in his place." They are opposed to any kind of change or sense of direction that takes the church away from what they want, and from their comfort zone, even if it is Biblical. Groups of powerful deacons are probably the main reason most older Baptist churches plateau and then go into decline, because they are built around pleasing themselves rather than reaching the lost.
If a pastor does come along who steps up and faces them toe to toe, and insists on doing things scripturally, he usually doesn't last very long. However, if there are enough people in the congregation who stand with him, and he can get into a position where he can change the church and restructure it on a Biblical model, there are long term, old line members who leave. In most cases, that becomes an open door to real growth, as the church is usually in a position, related to its resources, location and visibility, to do things that are outwardly focused instead of inwardly focused. The baptisty goes back into regular use. Discipleship grows and develops. Looks like that is exactly what is happening at FBC Durham, as it also happened at Capitol Hill Baptist Church, where Mark Dever is pastor. There is a record of success in the revitalization of Baptist churches that follow this pattern.