If all else fails, rather than applique over it, what about taking fabric markers and turn the stained fabric into a print. Use a fabric marker of a similar color as the stain and make something simple like three dots in a triangle shape (one dot on each point of an imaginary triangle) scattered over the patch. The stain can then become part of the fabric. And it if washes out over time, the dots won't look like a mistake. I love fabric markers for covering up boo-boos! :-)