That's a pretty elaborate theory, but I can't see it holding much water. Joe says time travel is "immediately" outlawed. There's no "buying a ticket." And Rian has established outside the film that the time machines can't be calibrated to a particular time or place, so she'd be shooting herself and her child into the past blindly, even if she managed to gain access to a machine. And even if she DID gain access to time travel, and was able to send them back to JUST the right time to "set up the timeline"...Cid would have to forget EVERYTHING and also become kind of stupid and not TK. Joe is no child genius, you know what I'm saying?
All that aside: look at Rian's writing. Is this a guy who makes a subtle point about motherhood, or a guy who has secret incest storylines built into his films?
I'm way too lazy to ever be truly belligerently insane.