Washing the batting doesn't shrink the batting, it the heat of the dryer. If you don't want the crinkly effect, soak the batting in hot water, spin dry, and the place in dryer. I would not agitate the batting. In my experience, you can only tell if batting shrinks when the quilting is heavy and the top and backing haven't been pre-washed.
the quilts where I pre-washed the top and backing have very little evidence of batting shrinkages unless I stipple closely.