I use batiks often and prewash all of them. Some bleed more than others and require changing the water a couple or three times to remove all of the excess dye.
To avoid adding chemical to the fabric, I think if you soak them (one at a time, or like colors together) in very warm water, swish them around, squeeze out the water, and repeat this process until the water stays clear, you'll have no problem.
Once the quilt is made and you wash it, you might (for extra insurance) use a color catcher, especially if you are wasing it with some detergent.
Someone on another thread awhile back said that the tried and true method of soaking in a vinegar solution does not work for batiks because the dyes that are used in batiks differ from the dye used in other fabric.