I am far from an expert in Biblical scholarship, but my readings suggest that there are three primary approaches that are taken when studying Bible as an academic discipline.
The first approach attempts to reconcile the Bible with archeology, philology, anthropology...(feel free to add to the ellipsis). When archeology was in its infancy in the 19th century, its raison d'etre was to prove the veracity of Biblical stories. So Woolley's excavations at Ur proved the truth of the Mabul, Egyptian archaeological chronology affirmed (or more accurately was made to fit into) a literal Biblical chronology, destroyed remnants at the site of Jericho must have been the wall that came a tumblin' down during the conquest of Joshua.
Then you have those that attempt to tear down the claims of the Bible by using the same disciplines. Many of the early Bible critics were anti-Semites who deemed it desirable to take away the uniquely Jewish claim to a God-given Torah. Julius Wellhausen was a card-carrying member of this group and it seems obvious that he had such an ulterior motive in his formulation of the Documentary Hypothesis.
Finally you have folks that take a truly scientific approach and try to look at the evidence objectively and through the lens of a continually improving body of knowledge in all of the relevant hard and soft sciences (including scientific disciplines that weren't even around 10 years ago, much less 100, such as studies of mtDNA variations.)
It is important to note that one's motivations says nothing about the veracity of one's claims. But while people in all three camps like to profess objectivity in supporting their respective claims - it is clear that only the third group demands of itself constant and expert scrutiny of its assertions and requires one to adopt the most reasonable explanation based on all of the available evidence.
I would put James Kugle - see How to Read the Bible: A Guide to Scripture, Then and Now - and Mark Zvi Brettler - see How to Read the Jewish Bible - into the third camp. While the frum velt may question Kugel's right to call himself "Orthodox", it is clear that he has looked at more evidence than the vast majority of people ever will, and as a result has presented many well-reasoned challenges to fundamental theological principles of Judaism. It is no longer sufficient to deny the claims of Biblical Criticism just because "that anti-Semite Wellhausen" was its primary progenitor (note that I am not making any particular DH claim here.) One must be able to challenge the sheer weight of evidence that supports a composite and fallible document, and not merely challenge Bible Criticism on a point here and a point there.
Unfortunately, there are too many barriers for most Torah Jews to be dispassionate in such matters since the threat of the abandonment of one's faith is usually seen as the ultimate outcome when fundamental beliefs are challenged, although Kugel and Brettler obviously disagree with this as a necessary consequence. The emotional anguish in disconnecting from one's community, the stigma of being considered an "outsider", the resultant familial discord, and the sheer existential trauma in the realization that one's Weltanschauung is a precarious foothold on the edge of a crumbling cliff, any one of these will allow cognitive dissonance to win out. Not only do such individuals faithfully resist all attempts at objectivity but at the same time they are often the most vociferous in their denial of doing so. The "Aish Hatorah/Arachim/Proofs of Torah" crowd exemplifies such a mentality.
Some will claim that Kugel and his ilk are guilty of dissonance as well, suggesting that they cannot fully reconcile the implications of their academic studies which should necessarily result in their taking the final leap of abandoning Orthodoxy altogether. The accusations will go so far as to assert that such individuals are no more rational than those who deny critical thought altogether. The mistake in such an assertion is that it conflates the Search for Truth and the Search for Meaning (which is also why I only criticize a fundamentalist theology - as promulgated by organizations like Aish Hatorah - for its claim to truth, not for its claim to meaning.) And the latter does not inevitably and deterministically derive from the claims of the former.