Hand embroidery is possible (and better looking) without going through to the backing, however when embroidering a sandwiched quilt like yours, you cannot avoid catching some of the batting in the embroidery stitches. The result down the road is that the stitching may very well pull the batting apart in places, weakening the quilt and creating loose spots in the embroidery.
Because this is truly an heirloom quilt, you might want to consider un-sandwiching just enough to make sure your embroidery catches only the top layer and not the batting. It would be well worth the extra time and effort.