Tosfos says that the Seder Olam says that she was three. Tosfos actually goes ahead and says that it can’t even be a mistake in the text since the whole conversation there is explaining how we get age. He only says that there are other Midrashim that argue.
I don’t understand how you can say about something that Rashi brings and accepts, that it doesn’t make sense on the basis of your “advanced” moral standards. If only you would have been around in Rashi’s day you coulda taught him a thing or two.