I use the Organic ketchup as well and I would definitely opt for a little extra sodium over HFCS.
I think ultimately you should do what feels right to you. Of course it's best to make home-made but if your lifestyle just won't accommodate that then, just do the best you can and see what works. If you see that you aren't losing weight or lowering your blood pressure, then something's got to go.
Maybe just try making some homemade ketchup, just once and see if you like it?