Most cheeses, not just cottage and other soft cheeses, are predominantly hardened casein. The remaining liquid is known as whey. It has some of the milk's proteins and almost all of the sugar. Commercial bakers love whey because it is indeed a cheap waste product, but one that gives a product many of the same nutritional and taste benefits of whole milk. If you are lactose intolerant, whey is one of the worst ingredients to encounter on a label.
Most allergies seem to be to casein, but many people are allergic to the whey proteins as well.
And of course, since the majority of the world's population is LI, by sheer chance many of them have protein allergies as well. It's not clear which is your problem, but you should avoid whey on a package label. See my SuperGuide to Dairy Products for more info on dairy. For your wife, not at all. There is absolutely no danger to the pregnant mother at any time, in any way.