It's pretty funny how Alison is lol. If Ian tells her that he liked the old hair more, she'll be like, "Oh yea, I just wanted to try it out. I'll probably go back to the old hair in a week."It's not a punishment. It means she feels more secure/less desperate so she feels comfortable asking him to wear the condom.
Same reason that she doesn't dye her hair if you are on her love route.
She's obsessed to the point of baby trapping Ian if he ain't falling for her. Crazy ass chick, but damn if she isn't an interesting character we don't see often.