Having some recent experience with buying a bicycle for the wife based on color, I understand your pain. At least you don't have to get her multiple bikes-one for form and one for function.

If the bike shop misrepresented the color or misrepresented the presence of the decals then it was false advertising and expect them to take care of it. If your woman was overly excited about the "pretty bike," then buyer beware-paint the bike.

How hard is she going to ride it? Is it really going to matter if the frame warranty is voided?
As far as paying for paint, if you both picked it out she should have some part in the paint payment.

Good luck-you'll need it.