Recover iPad Safari bookmarks overwritten by iCloud
The only way is to restore from a useful backup, if you have one.

If you sync the iPad to iTunes and use Time Machine regularly, you would likely have the appropriate backup to restore from. In that case:  


Restore the iPad backup set from Time Machine from a date before you overwrote the bookmarks. The location of the backup is ~/Library/Application Support/MobileSync/Backup/ (you can get to it by pressing Cmd+Shift+G in the Finder and entering this path).  
Connect the iPad, run iTunes and restore from the backup.  


If you use iCloud Backup, then you can restore from iCloud and choose which date's backup you'd like to restore from. You can check if you're using iCloud Backup by opening the Settings app on the iPad, then going to the iCloud submenu and looking at the status right below "Storage &amp; Backup", where it would say "iCloud Backup is off." (or "iCloud Backup is on.", as the case may be).

In any case, keep in mind that restoring from a backup means you lose all application data changes after the date of the backup.

Also see Restoring from a previous iCloud backup.