The Gigabyte thing is probably a VRM heatsink. Usually it's not taller than a ram stick, and your picture shows the CPU cooler is able to go over the ram stick.
Anyway as far as the thread title is concerned, your GPU is fine and I don't think there is any other way to place it.
Even if you can't re-position the CPU cooler, everything will work fine. No need to worry about your parts overheating or melting.
Just curious, what is that long blue wire along the top of the case?