I don't know the quilt, but based on your description I'd say you have several options. I've started pressing my seams open a lot more now because you get a much flatter quilt top and it's nicer to quilt. So that's something you could do. You can't nest the seams when they are pressed open, but I find that you can still feel when they are in the right place and I always pin, so I get nice intersections even with the open seams.
Another thing you could do is what I think you're suggesting, which is to clip the seam allowance in places where you need to change the direction of the seam. I've done this once or twice, but not often. There was a guest on one of the shows (don't remember who or which show) who does this all the time, so it shouldn't hurt the integrity of your quilt.