I think what could happen--and this was inspired by your theory--is that Crichton could go back to the Royal Planet and spend time with Novia and them and the statufied versions of Tyno and Katralla. Maybe they'll find a way to freeze him or something (Jool isn't using her cryopod anymore), and then thaw him out at the same time was Katralla and Tyno. Then John can help raise his kid (unofficially), while Tyno helps officially.
After all, Katralla was in love with Tyno, but the kid is John's.
One of the oldest ideas has been to send one of the Crichtons home (home being back to Earth). Theory #2 is based on that, but not. OK, so they decide to pick a random Crichton, pack his bags, and send him away in the Farscape module. This Crichton finds a wormhole, and enters it. It does not take him home, however, it takes him to some kind of Peacekeeper-controlled territories. Not only that, but FS1 is taken aboard some unimportant PK captain's Command Carrier. And Crichton, faced with an alternative of death, decides to become a Peacekeeper.
Now, you're thinking, Wouldn't they know who Crichton was? I say not. Crais didn't tell anyone where he was going. He killed Lt. Teeg just so nobody would know. And Scorpius probably would not want PK High Command to find out he's been scouring the universe for one brain.
Theory #3, "The Crichton Squadron:"
In CDM, the hallucinations of Scorpius might have served as a sign of the impending Chip Arc. You know, the future shows itself as a lesser being in the present, and all that. What if the Problema Dois Crichton represents a kind of "lite" version of the main arc for this season?
Scorpius has a new New Gammak Base for him to go research with. He also has the chip from Crichton's brain to get the wormhole equations out of. That means he is undoubtedly testing any proto-wormholes he happens to create using those equations. Now, thinking realistically, who would be the best person to attempt to fly into a wormhole? Someone who's intelligent, can think for themselves, and has ridden a wormhole before: John Crichton. Crichton would be, to Scorpius, the ultimate wormhole jockey. Not only that, but Scorpius has the chip, which was in Crichton's brain! He has some of Crichton's DNA! Do you get what I'm saying?
He cloned Crichton, and will continue to do so, as long as he needs test subjects! At Scorpius's New New Gammak Base, there is now about 500 Crichtons just milling around, waiting for an assignment.
John has been duplicated, but Harvey hasn't. So...Harvey now sees his chance to take over
from Crichton nr 1. Chiana, who still has feelings for Ol' Earthboy decides that the D'Argo era
is gone and teams up with Harvey.
What is Harvey up to? Harvey wants his real body, Scorpius' body.