Actually, I think the large stitches add to the charm and character of the quilt.
I saw an entire book about the kind of straight stitching of applique shapes you are talking about. This was a very popular method of doing applique when sewing machines were still relatively new and is a fully acceptable method. However, it seems to me you would have a problem trying to twist and turn that entire quilt top under the machine (since it's not individual blocks anymore) to stitch around the edge of each applique.
Personally, I'd add back the big stitches on the one petal you re-did byhand and just move on to actually quilting the top.