Interesting thread hmike, I shall be following even if I'm not able to take further part. For now, I'm short on 'serious thinking' time so for a start at least, here are some non-intellectual thoughts of mine:
Why, if God didn't 'protect' the Scriptures, should that mean he doesn't exist? 'Protection' to me doesn't necessarily mean maintaining a status quo. Perhaps God has allowed that leeway - I'd suggest maybe to encourage his followers not to take the Scriptures too seriously/literally. As many of us here know, if you take the Bible literally, you quickly tie yourself in knots trying to explain the contradictions! Yet if believers came to realise and accept that there are scribal errors etc, it wouldn't be such a big deal to them to try and protect the Bible from 'attack'.
For the believer then, I guess the dilemma is what to do with the problem verses - ignore them and hope they go away is probably the most likely response I'd see from many of the folks I know. Sad really, no wonder groups like the JWs can come along and use 'regular Christians' for target practice - a lot of us don't actually know how to explain what we believe!