What was your stitch length? I usually do straight stitching at 3mm. That isn't terribly hard to pick out. If you pull out all your stitches, I'd re-do with that stitch length. If you did some at 2mm & switch to 3mm for the rest, it will be very noticeable. As for pressing with the quilt sandwiched, I think that will be much more difficult than pressing a single layer of fabric but you can give it a try as long as your batting is 100% wool, 100% cotton, or some combination of those two. If it is polyester, poly blend, silk blend or has bamboo/rayon, I'm not sure you'll get your iron hot enough to really get the fabric pressed well. You can give it a try, but if your fabric doesn't end up stiff like a piece of paper, you may end up with the same problem all over again (meaning twice as much to pick out).