I had planned on expanding this into a few posts, but I'm short of time.
I think the ban is purely a protective measure. When is the last time you heard in a shiur "Well, yes, the Rambam says that. But we don't pasken like him, so just forget about it, don't read it, and we'll move on." I'd love to see a talmid say that to his rebbe, "Yeah, since we don't pasken like X, so I decided not to prepare his view on the sugya, after all, its kefirah."
Leaders are supposed to lead, and that means making decisions. We do it for our children all the time. They can't understand certain things, so we tell it to them on a simple level. A doctor discloses information to his patient, but tells him the basic truth. He doesn't delve into the exact numbers of every study done on a particular procedure or medication. An attorney discusses matters with his client, the pros and cons. But he won't get into a long theoretical discussion on the merits of securities law. Its pointless.
Most people are sheep. They follow blindly, either because they can't do or don't know better. And for them, we make decisions. Hopefully, at the proper time, they grow up and we introduce them to more complicated ideas. Elitist? Perhaps, but am I wrong? And some of them never grow up.
Does anyone doubt, that you could make statements, fully compatible with Judaism's beliefs, which would throw off a huge segment of the Charedi world? Or the MO world? When you have the view that Chazal are infallible, something like R' Slifkin's works can be very troubling, and very damaging. Not are, but can be. Would you publicly state everything you feel, knowing the consequences could be people leaving Judaism?
Do you think Godol Hador would go to a class of 4th graders and say to them "There was no global flood. Maybe it was local. Oh, and Yetzias Mitzraim, it wasn't really 600,000 men."
So they issued the ban. Look at the reasons written in the ban, and in the letters that followed. R' Slifkin's works could lead to a lack of trust in Chazal. Now, for me, they only increased my trust in Chazal. I recognize that they are humans (a rather inspiring thought), who could err, yet still accomplished great amounts. That they utilized the science of their day, just as we should.
In the latest letter, RSK is said to have signed it because the "tone" of R' Slifkin's works were problematic. Tone? That has nothing to do with content. Nothing to do with ideas. Only the consequences. Post-ban there were rumors that some of the signers had been tricked, they thought it would only be shown to Slifkin, not that it should be called kefirah, that he should rephrase his works. Tone, not ideas.
Societies change slowly. 9/11 wasn't a great change, it was the recognition of something that had been going on for years. Now, there are vocational schools opening up in Boro Park, talk of the Tal law in Israel, Touro College too. And there are more changes. The Internet wasn't banned in Lakewood because it was unknown. Everyone carries cellphones (unless you're in the Mir). These things start out at the edges and move in. And they're still at the edges. They'll route around the roadblocks, and "pretty soon" it'll be "normal".
We're at this impasse because of the failure of our educational system, among other things. So, for now, some rabbonim have decided that people shouldn't hear. I happen to disagree, but I can understand their point. They have a society, and they feel that this can destroy it. That they went about it in a terrible way is another story.
Obviously, its not so clear cut. Practically, Slifkin's books wouldn't be read in Meah Shearim or Bnei Brak. So why ban it? I don't know, but I'm just giving an alternative view on it. We could be really cynical and just say that all the signers were tricked, never really meant it, and this is the work of a few people who deserve to get taught a lesson.
I'll make a prediction. In fifty years, or maybe a hundred, modern science, the age of the universe and evolution, medicine, and the Earth circling around the Sun, will be accepted in Charedi circles as well. As people learn that science is not evil and that it enhances religion, they will come around.