Gaga wasn't nominated that year for Best New Artsist though
She couldn't be nominated because the rule stated that if the artist had received a nomination in previous ceremonies said artist wasn't ellegible for Best New Artist. Just Dance had been nominated the year before in one of the Dance/Electronic categories, thus she wasn't ellegible.
They changed the rule BECAUSE OF GAGA, which was kind of unfair, but she didn't receive any benefit from said change which happened in the next ceremony after that.
However, maybe they did offer Gaga the opening as a way to capitalize on her fame(this was during Bad Romance era) and a way to "reward" her on missing our on such an important award as Best New Artist.
Kanye's comment is kinda weird.