Any water leak in a house is a big deal although perhaps not so much for continuation of the roofing job. If they stripped it down to the decking and the decking is now wet, all they have to do on a good summer day is to wait a couple hours and the breeze and the sun will dry it up enough to continue the work. In fact, it is even easier now that it's all stripped instead of just part of it being covered with shingles and part exposed where they would have to make sure the top edge of the shingled part is sealed.
The internal damage, however, is a different story. What is the extent of the internal damage? The roofing company is responsible and would have to work with you on resolving the situation, including repairs, compensation and all the way up to putting this on their liability insurance, a copy of certificate of which they would have provided you with the rest of the paperwork before commencing the job. Document the damage if it is significant, take some pictures. Let's hope this does not turn into a legal battle but you should be prepared to produce proof of the damage you claim happened as a result of the roofing company not taking precautions.
Once again, if by "no big deal" they meant the actual roofing job, this makes sense. For a one time occurrence, they should just let it dry out and continue.