The first time I had this happen I culled the doe, the litter and the sires. Like you, I did not think it was worth the risk to start my new rabbitry with sick rabbits. I picked up a new rabbit (different breed) about six weeks ago, and it started sneezing last week. She is in isolation now--which is a completely separated from the rabbitry.
I plan to breed her to a buck that will be used for her only, and grow out the kits and see how their health is. Some breeders tell me that snuffles is not so bad, and that rabbits recover from it. I think the symptomless rabbit becomes a carrier and passes it onto some of the kits, so this theory will be tested. I will not sell from this line, and any that display illness will be dispatched immediately. I will replace her with a "healthy" kit, and test again. In the mean time, I get compensated with some meat for the family. Still not sure if it worth the cost of the feed...but I have rare breeds, and they are hard to get and seem more susceptible to illness.
I do not think I would go through the trouble with a more common, easier to get breed.