How should we view contradictions between modern viewpoints and Chazal/Rishonim

There are many places where the simple understanding of Chazal and Rishonim contradicts the modern viewpoint. There are 3 ways to deal with this:

1. We only have what Chazal and the Rishonim told us. It doesn't bother us at all that there is a contradiction
2. The contradiction bothers us, but it's not really a contradiction because the real meaning of Chazal is in synch with the modern viewpoint
3. The contradiction exists and we need to solve it somehow

To stereotype, hard core Charedim believe 1, left wing Charedim/RWMO believe 2 and OO believe 3. 

A good example of this is the attitude towards women. As I pointed out in my post The Maharal's view of women - inferior, the Maharal clearly and unequivically views women as inferior to men, and it's not just the Maharal, this is the viewpoint of Chazal as well. The hard core Charedi view accepts this and therefore views women's eduction as an עת לעשות לה' הפרו תורתך and prominent Rabbanim like R' Wosner wonder how we are permitted to have Beis Yakkov schools for girls. The left wing Charedim/RWMO are very well represented in the comments on R' Eidensohn's blogs asking why he is publicizing these views and feeling very uncomfortable with them. This group also comes up with various apologetics explaining how women are holier then men etc. The last group, OO, simply accepts the contradictions and moves on from there"innovating" with things like womens minyanim, Rabbahs, etc.

Another good example is Torah and science. Hard core Charedim believe that the world is 6000 years old, the Mabul was a world wide flood that destroyed everything and 2.5 million Jews left Egypt. Left wing Charedim/RWMO, on the other hand are bothered greatly by these questions and come up with various unconvincing apologetics to explain them. The OO crowd on the other hand simply accepts what science/archeology says and moves on (see thetorah.com for many examples of this). 

As I mentioned above this is a stereotype because even the most hard core Charedim have been affected by the times. The place we can see this most clearly is marriage. The Gemara states that a woman has certain obligations to her husband, for example, washing his hands and feet and serving him. These are quoted l'halacha in Shulchan Aruch. The Rambam even allows the husband to hit his wife to force her to fulfill these obligations. Not even the most conservative Charedim approach marraige this way today. 

R' Aharon Lichtenstein put it best where he writes:

How and why do we depart from positions articulated by some of our greatest -- "from whose mouths we live and from whose waters we drink" -- and, is this departure legitimate? Are we victims of the Zeitgeist, swept along by general socio-historical currents?

My answer is yes. There is no question that the values of the outside world have infiltrated even the most sheltered Charedim. The question is how will this play out. At some point, 1 becomes very difficult if not impossible. and 2 also becomes untenable as the apologetics become more and more unconvincing. Where does that leave us? Basically where I am, a lot of questions and no answers.