Actually, I agree with Naruto. The Kyuubi doesn't seem to know what this war is about, or who is fighting it. It is the entire ninja world versus Akatsuki.

The enemy is three guys: Madara, the plant dudes, and Kabuto (who is a wildcard at this point, anyway). Naruto won't bear the hatred of an army if he wins. Just the "hate" of Akatsuki (who have treated Naruto as a strategic resource for about 400 chapters now, anyway).

Madara is too "smart" of a villain to actually "hate" Naruto, anyway.

If anything, the Kyuubi wants Madara to succeed, so that he can join up with the rest of the Jyuubi; and his speech is just a lame tactic to make Naruto's spirit fail him.