A lot of the time there is no difference between feeders and fancies. Some folks will tell you that feeders are inbred, but in reality, without buying mice from a lab-type company (who track the line breedings), fancies are just as prone to being inbred as feeders.
It sounds like your problem may have been a result of keeping them on pine. Any phenol-type shavings (ones which contain natural chemicals and emit strong aromas) are toxic and do contribute to respiratory diseases. Your best bet is to use some other type of bedding.
However to answer your question if it is safe to feed these mice to snakes (the ones with respiratory infections), the answer is yes. The respiratory infections will not harm your snakes. Although, I will not feed my snakes prey that have been raised on pine or cedar--or at least I try not to (just because of the toxic nature of these plants).