If it is an important quilt, I always preshrink the batting. I only wet it and dry in the dryer. If I had stinky batting, I would lay it out in the sunshine before I did anything. I'm no expert, but I would consider baking soda or vinegar before anything else.
I had a bag of stinky potting soil that I left on the sidewalk beside the house. I opened it and dumped it into the bin, and then realized it stunk. My online buddies suggested air and sunshine, saying something about aerobic something or another. I would assume the same advice might apply to the also mostly organic batting.
bkay