That’s what I said! 
I was agreeing with you!
Though my mitochondria think you’re an idiot, for some reason.
No, no you got it all wrong. Mitochondria prefer slavery, they are happier being kept as slaves. They wouldn’t know what to do as free living organisms.
That’s what all the tyrants say…
Found it: “Lord of Hosts,” by Connie Willis. Published in Omni Magazine, June 1987. Whole magazine text is available here, although it looks like OCR with some errors here and there. Search the page for “lord of hosts,” and you’ll find the start of the story.
Short version: it wasn’t the Second Coming. Instead, two people had died, and as they waited in some sort of limbo, one was quoting bible verses to the other to support his claim that the mitochondria were the ones who would be going to heaven. The story ends with the mitochondria coming out of their bodies to be received in heaven.