I would wait until the puppies are at least three weeks old. When you do bathe her do not use soap and be sure to blow dry her thoroughly on a warm stting to keep her from getting chilled. For now, you can use baby wipes to clean her up and cut down on the smell.
If you are a dog and your owner suggests that you wear a sweater, suggest that he wear a tail.
If it's the mother that's smelling so badly, I see no reason not to give her a bath now. I would be a little concerned about why she smells so bad. Is this normal for her? Make sure you rinse her really well, and dry her really well, in any folds or creases, and her feet.