Can iCloud's Documents and Data be configured to sync on a per-app basis?
You can disable iCloud on iWork by going to the Settings app, and scroll down to the install apps settings, you will find each iWork app has it's own section, Pages, Numbers and Keynote.

In each iWork app's settings there is an option "Use iCloud". Turn this to off, and keep the Documents and Data in the iCloud menu on.

For Mac, the iWork apps do not support iCloud Document Sync. (If you enable sync on iOS, the files created on iOS will download into your library, you can't open them however, and you are unable to upload to iCloud in iWork)

In Mountain Lion they will, but it appears that iCloud Doc sync integration will be at the OS Level, rather than iWork app level. Instead being more like DropBox* where you have an area (I say area, because it's not a folder, but it's quite similar to one) for iCloud.

*Although this area only seems to appear in Open/Save Dialogs, and will only show files that are registered to the App.