You should backup the whole folder, not only the keys.
In case of troouble, you can just load up the wallet file(s), because if you import a (another adress') key into an existing wallet you will indeed end up with a wallet with 2 addresses.
I actually happen to have lot of wallets loaded up in the multibit client, and have backups of all the keys, but after loading them back with the keys, an extra address gets added. Now I am not sure if that will automatically be aded, next time i import a private key.