I guess the transcripts won't mention this, but Rodney has more than once aimed a gun over his shoulder and fired multiple rounds without looking at his target. He did it to possessed John, and he recently did it in the opening of Sateda.

In The Long Goodbye, I'm pretty sure John's lucky and/or skilled enough not to get shot in the face.

I agree with your interpretation; I also think Rodney can't watch himself killing human beings. I'll have to rewatch again, but he might have been genuinely bothered by the mouse in Common Ground, given his reaction to rodents in Hide and Seek and Duet. And Letters from Pegasus establishes his childhood attachment to cute mammals.

I'd write it off as a quirk after two seasons, but returning to it in the third season makes me think it's a consciously chosen theme.