Its a little late now, but if you had sliced, I think it is called scything where the back of the leather is removed at an angle, then the seam could have been overlapped and and been much less evident. Also the edges next to the hardware could have been done the same to allow a better fit. I am no leather worker but have seen that process done. It might not even work on something as small as a pen. How about using a lighter or softer leather? I hope you do find some good answers to your problem, John.
Charles