I realize you're not looking for a review of the article, however, I can't help but note a few items.
While the author highlights a problem within the general evangelical 'Christian' population that views faith and reason at odds and also correctly identifies secular humanism as a "religion... without (God)." there are some general historical errors of this piece, i.e. "Martin Luther and John Calvin approved the slaughter of Anabaptists..." and the reexamining of history though a specifically anti-religious lens, "A third of the population of Germany perished during a single 30-year doctrinal dispute between Catholics, Lutherans and Calvinists", suggesting that a single doctrinal dispute separated those groups and caused the chaos that was ultimately the result of the leadership of the countries involved and had little to do with issues faith.
That said, I think the author improperly views Christianity as a religion based on faith, as if faith was opposed to reason. It is evident they do so based on many Christian's view of their own faith as a subjectively embraced experience, rather than a reasoned understanding of the historical fact of Christ and His work. The author's example of President's Bush seemingly direct-from-God order to invade certain countries is evidence of this idea.
The question before us is not whether faith is legitimate or which faith is best. It is: Shall we allow the divine experience of one group to control the behavior of those with a different experience?
Let us work to see that the answer to that question remains an unequivocal, "No."
How far do we take this? We've reached the point in society where "murder" is defined as matter of faith, not reason, as is the case in abortion... I think Van Til was right, at least on this issue, its not "if god" but "which (G)od". A society whose morals (as if there can be "morals" in a system that accepts and promotes secular humanistic evolution as a fact) are subjective, based on the whims of the majority is only a short step away from anarchy.
It is important for us to strive to express our faith in reason-based, fact-based and history-based ways and to encourage other believers to think likewise. Christ is not some subjective personal thought, but rather a collectively embraced historical figure who really did what the Bible claims and thus our faith is based on real events that really accomplished what God declares in His Word declares they did.
Also, when Scientific "facts" seem to indicate something different than what the Church believes the Bible states, perhaps it is the interpretation of Scripture, rather than the Scriptures themselves that are at odds with the universe. For example, the Roman Catholic Church taught that the Earth was the center of the universe and that the Sun and other solar bodies orbited around it. They seemingly took this belief from Scripture, claiming that certain verses taught it ( http://radongas.blogspot.com
This revamping of tradition can only be taken so far, however, there are certain things clearly taught in Scripture that may not be apparent in the revealed universe. Theistic evolution, for example, is an attempt at revamping the first chapters of Genesis as to conform to a proposed scientific theory, diluting both concepts as to make them untenable. This leads to concepts such as "intelligent design", which is not Biblical creation. While I admit that the Bible shouldn't be used as a scientific text, it is usually our tradition, not Scripture which conflict with the "evidence" science discovers in the world around us. ( http://news.yahoo.com/s/ap
One final example of the type of problematic tradition that may be overturned by scientific discovery has to do with the potential for genetic pre-disposition toward homosexuality. For years evangelical Christians have argued and continue to argue that there is no, cannot be, will never be found a genetic marker or clue for a predespotisition for homosexuality, yet if (and when) such a genetic link is made it could only be denied by those Christians. I however view this staunch evangelical view as founded in tradition, not in Scripture which teaches that we're all "born in sin" and dead in Adam from conception... the fact that one may have a genetic disposition toward one sinful expression of that deadness or another should therefore not surprise us.
To reiterate then what I said previously, it is of the utmost importance that we who recognize the false-dichotomy between faith and reason seek to establish and express the true nature of faith as grounded in reason and the facts of Scripture and history and yet maintain faith as a supernatural gift of our Lord.