You can disable auto backups in iTunes by using a free program called BackOff.
link: BackOff Speeds Up iTunes Sync for iPhone, iPod Touch and iPad
Backups were taking a really long time for me too. I think the problem was all the manga I have in ComicZeal... 6gb+ of 3k+ cbz comics, which ComicZeal unarchived so it was like 70k+ images to backup. After 3 hours of backing up I was only at 15%.
Note that with BackOff you can still manually start a backup by right-clicking on the iPad and selecting "backup".