Quilts are often finished with a combination of quilting methods. They are described simply as 'hand and machine quilted', not 'part hand quilted/part machine quilted'. I think your idea and reasoning about adding detail to the appliqué with machine quilting is very suitable, especially since it was machine appliquéd. A simpler hand quilting pattern, as long as it suits the overall quilt design, would draw even more attention to the appliqué.
You could always try it on just one flower appliquéd to a square of the white as a test run to see if you like the effect of the two methods together. I certainly don't think mixing them would lessen the intrinsic value of the finished quilt any, not in this day and age.