I am having exactly the same problem.
I backed up my iPad 1 which is running iOS 5.1.1
I also made sure that I had a copy of all my books in iTunes.
I then deleted iBooks 3.
I rebooted my iPad.
From the iPad opened up the AppStore app and re-downloaded iBooks.
I attempted to start iBooks and it again crashed.
I deleted iBooks from the iPad and rebooted it.
In iTunes, I did a restore from the Backup.
I again attempted to start iBooks and it again crashed.
FIXED - FOUND SOLUTION:
I backed up my iPad to iTunes.
I deleted iBooks from the iPad by holding down the iBooks icon and choosing delete.
Since I had a backup I wasn't concerned when it said it would delete all the data associated with this app.
I plugged in my iPad into my Macbook Pro.
I opened iTunes on my Mac and under "Library" I clicked on Apps.
I found iBooks and dragged it over to my iPad listed under "Device".
After it was finished copying, I went into "Settings", "Apps" and chose iBooks.
I turned off Show All Purchases to OFF.
The note under it says: "Sows purchases availabel from the could in your library. iOS 6 or later is required.
I can understand your frustration, and I'm sorry to hear you are unable to get things working.
There is a possibility that there is a glitch in iOS 5.1.1 and when I restored it, and it automatically synchronized, I am wondering if that is what got it to work.
If it is a problem with the iBooks app, and it is now working on my iPad 1 using 5.1.1, then why is it working now?
Therefore, I don't think it is a problem with the new iBooks app.
As an iOS developer, I do understand that there is a possibility that the data needs to be re-synchronized and often apps upgrade the data structure during the synchronization process.
I have my iPad automatically syncrhonize and I didn't put that in my previous comment.
Possibly if you try it again, it might work if you do a synchronize afterward.
As I understand the iBooks app will have a signature that will only work on the iOS device account it was purchased to run on. I don't beleive it will work if you get a copy from someone else.
Since you are on Windows, once you are able to get your Windows machine, you can probably find iBooks 2 by using it's file Explorer and doing a Search for iBooks 2.
Then you can attempt to copy iBooks 2 in place of iBooks 3.
You might want to make a copy of iBooks 3 before you delete it.
As I did not have time to sit and wait for Apple to fix this, I connected my ipad to the computer and went into iTunes and selected "Books" from under my device. This shows a list of the books that are on your ipad.
I then systematically started deleting documents a few at a time, and trying to open iBooks on the ipad after every set of deletions. Eventually, after I deleted about 30 documents, iBooks loaded and is not crashing.
I started with books that I had purchased through itunes, none of those seemed to be the cause.
From there, the rest were all regular PDFs.. So, from what I've seen, the cause is likely something about particular PDFs that is causing iBooks to crash.
For anyone that needs to get iBooks working immediately, I would suggest backing up your device to computer, and then go through the list of books on your device as I did and start deleting a few at a time, trying iBooks to see if it crashes between every set of deletions.. Note that unless you have copies of the documents elsewhere, deleting the books this way does DELETE them and you will need to move them back onto the ipad from your original sources.