The main reason is that iTunes doesnt have a wy to view books that were purchased. iBooks was written for that which is why it makes sense.
The bg reason that Apple doesn't split off the stores like that is Windows. Apple doesnt want to write other Apps to Windows doesktop viewers (note there is no iBooks for windows). iBooks is a new market though compared to Movies which hs been around for longer.
iTunes has no problems playing movies on both Mac and Windows. Unless you think iMovie is comming to Windows anytime soon, things won't change (and iTunes isn't going to remove video playback either).
Futhermore, iMovie isn't a library manager on the same level as iTunes is. I'ts not comparable.
Rewriting windows versions wouldn't be difficult, in fact Apple would be remiss not to offer them - music, movies, books, etc. and with their move to iCloud based iWork app's, Apple has their eye on offering a better experience for non-Apple users to try the "other side" for years.
iBooks wasn't offered on OS X due to publishing rights and DRM, and I know that Apple has been working on an iBooks for Windows app for a while.
iPhoto and iBooks are already separate app's. iPhoto allows users to create and order their own calendars, books, etc., would it be so difficult for iMovie (or one dedicated app) to purchase movies/television programs, thus leaving iTunes to handle music?
Let's recap:
1. iPhoto and soon Photo's is separate
2. iBooks is separate
3. iTunes was built to handle music, keep it that way
4. Keep iOS App management in iTunes (simple)
so
5. Add a "Film" store to iMovie or simply produce an app for film
Revamp "iSync" to manage the media, just as iTunes. Easy to remove such code and produce one simple app based on iTunes management and iSync, develop it until ripe.
Done. Apple has been slowly adding more iTunes functionality as media increases, now they are separating app's based on media. Heck, they don't even need to create an iSync app, just have iTunes remain the conduit but remove the added media into dedicated applications for Mac AND Windows. Windows users can purchase those app's (or make em free, they'll still have higher sales volumes), at best enticing them to try a Mac. Win/win.