Even if you disable the GPU in software unless you directly alter the fan curve the fans are still going to spin erratically unless it supports a 0RPM mode.
You'll still have to manually unplung PCI_e power from the GPU but as Cyracus has alluded to you can tell the BIOS to default video out to the iGPU instead of PCI_e (why the screen is black on start). If your monitor has multiple inputs you could also plug two cables in. Make it so you don't have to do that manually every time.