"B-But Wario only cares about money!"
In this situation, money was simply the original motivator. While, yes, his actions are questionable, Wario is still a person. As a character, he has emotions and feelings besides greed.
They really do have quite a unique relationship, don't they? I mean, it's one of the few times we've seen Wario show some genuine emotion, namely the laugh the two share at the end.