It is possible that because of the distinctive feature being publicized worldwide, that Madeleine cannot be disguised enough to take outside, and that the abductor will kill her to prevent her from being recognized if kept.
I have no idea whether contact lenses would hide the defect. (I hate to call it a defect, but that's how it has been referred to in the press, and I can't think of another way to describe it right at the moment.)
If so, you would think authorities would ask eyeglass shops in Portugal and Spain, at least, to let them know if someone orders colored lenses that do not have a prescription in them.