So far, most protestants keep on defending what they do as scriptural. Catholics and charismatics know that's not necessary. Long before Luther, and ever since then, the best way to justify authority is by appealing to church tradition and/or divine revelation. Fighting over Bible verses is the least stable by far! However, since appealing to scripture IS the protestant tradition, I predict those appeals will focus more and more on extracting *principles* of scripture. The truth is spreading too quickly - New Testament churches were far different than most today.
At age 21, my primary motive for studying NT events in chronological order was to observe (and yes, to support) a more primitive ecclesiology. I still feel that's valid, but I've also been on record for several years that we are not bound to follow "what the Bible says". For one thing, that's insulting to God. For another, some of the strongest patterns we can observe consistently in New Testament church life still aren't remotely uniform. Even in century one, it seems, the Lord didn't "follow the Bible".
Christians reading the scriptures ought to see the primitive church as it was, and then prayerfully decide how to follow the Lord into church life today. Personally, I've never met anyone who does church exactly like any of the NT churches did. So that's not the point. On the other hand, most christians never even get to see such a clean view of the first century. The view most promoted is usually the one church authorities believe best supports their own way of things.
In 2009, it seems like faith-based Biblical Studies ought to have, by now, reconstructed one cohesive "things most likely happened this way" view of the New Testament's total historical context. Instead, what we have is pockets of support for various denominational traditions. Thus, in a way, christians have hijacked the bible far worse than the most anti-faith skeptical scholar could ever hope to. Being mutually respectful of one another's traditions doesn't serve truth in scholarship, either. (We might accept tradition in practice, but it shouldn't have first place over scholarship.)
Although it frustrates me that faith based research in the Academy still has to battle against too many premises of the Enlightenment, I feel far more comfortable planning a trip to an SBL conference than I do walking onto any Seminary campus. At least, so far...