Those intersections can be really fussy. Sometimes it works for me to pin parallel to the seam and as it approaches the needle, withdraw it very slowly. I also sew with an open toe foot so I can see the pin get pretty close to the needle first.
But in all actuallity, I don't mind twisting the seam. Makes quilting in the ditch a bitch, but if you press well, you may never be able to tell. I would not clip the seam.