I have sometimes considered theological studies at a liberal or secular institution like IU or Yale, but have always stayed with more evangelical institutions (Houghton, TEDS, Covenant). Part of it was wanting to be fed and to grow spiritually through my educational pursuits and the other part is not wanting to fight my way uphill all the time as a theological conservative (relatively speaking). I wonder, though, if part of the reason is fear - wanting to guard and protect my faith.
Last night I took a break from reading John Williamson Nevin (an obscure American theologian) to read a biography of Adolf Schlatter (
Adolf Schlatter: A Biography of Germany's Premier Biblical Theologian
) (an obscure German theologian). I was struck by the decision making process that led Schlatter into theological studies as a University student. At first Schlatter steered clear of theological studies, arguing "Theological study is dangerous and could easily shake one's faith." Of course, German theological study was mainly of the highly critical nature, so his concern was legitimate. However, his sister was of a different opinion. She argued that to avoid theological studies for this reason was cowardly and faithless.

Schlatter eventually changed his mind and pursued theological studies, concluding that "if I avoided theological study out of fear I would not be preserving my faith but actually giving it up." Again, "I came to the conclusion that avoiding theological study to preserve faith was rank hypocrisy, and this conclusion brought decisive consequences." His biographer goes on to write that Schlatter's anxieties were not without foundation, and his studies did bring him to a crisis of faith where he even doubted the existence of God. However, "he also insisted that to act solely on the basis of this anxiety would not be an act 'from faith' because it would fail to take account of the capacity of God's preserving grace."
I understand Schlatter; yet, I think there's another truth that we must hold in tension with this. There seems to be plenty of encouragement from Scripture to 'guard your heart', to protect oneself from false teaching, etc. There is a 'garbage in, garbage out' dynamic to be on guard against.
How do you balance these two seemingly conflicting calls - the call to guard oneself vs. the call to have faith in God's ability to preserve our faith? I don't know, but it seems like a healthy dose of honest, self evaluation is important. I think it would have been unwise for me to have sat under and allow myself to be taugh by liberal/secular theologians during my undergraduate years. I had more biblical/theological training than most undergrad having grown up in a pastors home. However, it wasn't of the kind that exposed me to critical objections to the Bible and to the Christian faith. I would have been unprepared to handle them. At the same time, now, I think it would be faithless to steer away from such interactions simply out of fear of losing faith (though the fear of doing the work and not being granted a degree because of a conservative outlook is very real).
Here again, in this tension, we run headlong into the tension between God's sovereignty in preserving us and the call upon us to keep the faith and not allow ourselves to be shipwrecked. I don't think there is an easy way to remove the tension, and I think the Bible is intentional on that.