Ok, I understand your contacts ont he MBP are the way you want them, icloud.com is wrong, and you have a backup; just in case. If I'm right, then this should do the trick, and you've got the backup in case I'm wrong.
Turn off Contacts in your iCloud settings on the MBP. Make sure you tell it to keep them, if prompted.
Do the same thing on the iPad, but tell it to discard/delete them.
Go to icloud.com in Safari.
Click the red ribbon to see the Groups page and make sure you've got All Contacts selected.
Click on the cog/gear icon at the bottom of the contact list and choose Select All.
Click on the cog/gear icon again and choose Delete.
That should clear all contacts from icloud.com. Go ahead and leave the web app and go back in, just to make sure they are all gone.
Now, go back to the MBP and turn on your Contact syncing in the iCloud settings. Pay close attention to any dialogs. You'll want to Keep or Merge contacts. Don't accept anything that says it will delete them off the MBP.
Give it some time, the more contacts you have the more time, then go back to icloud.com and make sure it shows the right contacts.
When the database looks good go ahead and turn your Contacts syncing back on in the iPad's iCloud settings.
Good luck.
Absolute worst comes to worst, it is possible to take the vCard file you made and import it in the icloud.com site. For the iPad, you can mail the file to yourself, then tap and hold the attachment in Mail for an option to import the contacts.
The problem with this method is that it may cause duplicates when you try to sync the devices again. Then again it may not. They are supposed to merge, and if the contacts are identical they should. And you'll probably lose any groups you have set up using this method. The vCard file only stores the contacts themselves, not group relationships.