Higher load tires are designed for a heavier vehicles. Some complain of a rougher ride depending on the tire. Shouldn't have anything to do with balancing, but I would think a E's sidewall would be stout-not flex and may balance easier. If you have a choice a C will be better suited for a lightweight jeep.
FWIW.. I bought stock rubi wheels for my Tj sport that came with MTR's. I replaced them with the same tire which was load E being a 16 wheel. Hated life and eventually switched to C duratracs.
Now with the Jk I'm running E rated Hankooks and don't have the issues I had with my Tj. The rubber is supposedly softer with the tire and doesn't ride all that bad.