How much input did Gene actually have on TFF? In spite of the "executive consultant" credit he was getting at that point, it doesn't seem like he had much influence on the films post TMP. Not to mention TNG probably had more of his attention in 1989.
Everything I ever read about TFF indicated it was Paramount that was skittish about Kirk and company encountering god and Satan, and watered down the script. Never mind Kirk already met the devil on Saturday morning tv in 1973. ;)
Superbeings who were once viewed as gods (or devils) in ancient times was a recurring theme in TOS, the animated series, and some early TMP script treatments.
Few fans ever seem to notice TFF has similarities to the animated series episode Beyond the Farthest Star. Both have powerful malevolent entities imprisoned on dead planets, who wish to use the Enterprise as a "body" to escape their prisons.
I was under the impression Sean Connery Sha Ka Ree was simply weakened by the Phaser barrage, losing it's cohesive form, not actually destroyed or killed.
We can continue this over in the Star Trek thread if you'd like?