The Yellow Crayon scene is one of my favorite scenes in the series. And I'm not sure it would have worked with another character. Buffy would try to fight Willow, and Willow has shown that she's psychologically able to fight Buffy. DarkWillow rejects Giles, so he wouldn't have the emotional power over her to do it. Anya and Willow were never especially close. Dawn would probably have run away -- and even if she hadn't, having the powerful adult beat up on the kid would have alienated the audience too much.
But Xander is not only her longstanding best friend, he's a man. And the scene plays off traditional ideas of gender, which are often challenged in Buffy but also from time to time reaffirmed. It matters less that Willow hurts Xander than it would if he were a woman or a girl: a man is expected to be able to withstand anything a woman throws at him. And at the end, Willow is reduced to pounding on his chest -- an utterly futile gesture, as she certainly knows. Everyone knows BtVS is about strong women, but what gets rather less attention is that one of the things it repeatedly says is that strong women still need strong men -- and this, more than any other, is the scene where Xander gets to be that strong man. (Giles, Angel, Riley, and Spike routinely do.)
