I really do not want to do that. Besides, it does not help with synching the bookmarks in my iPod to preserve them by copying them into Safari's bookmarks on the Mac. I want to control what folders I back up. Many of the bookmarks I have on Mac Safari are not suitable to use on the iPod. Sync between devices llke that does not allow me control to copy only what I want.Because no one but you has a private stash of bookmarks.
One thing you could do is drag the folders / bookmarks you don't want synced and put on your Desktop or some other location, your Finder Favorites or whatever, you can still just as easily double click on them and go to those sites, but they just don't live inside Safari.
You may synchronize your external bookmarks using Dropbox, OneDrive, and the soon to be released iCloud drive.