Muslin comes in dozens of types & qualities, so perhaps the one you selected wasn't the best choice for your project. You might try spritzing with white vinegar & pressing to see if the wrinkles come out. As far as the finished quilt, if you use a cotton batting and wash you are going to get a crinkled look that will minimize the wrinkles. If you haven't started yet I think I would look for a better quality muslin. You are going to put a lot of time and effort in.
I've used Southern Belle and a higher count Roclon muslin and have been happy with the results.