He doesn't have to face C'baoth and fight with a Clone.
Somehwere in the Thrawn trilogy, Wedge mentions the existence of C'baoth and he heard from Republic forces. Maybe Galen went on a scout mission and found C'baoth? The crazy Jedi doesn't have a lightsaber when he faces Luke, so Galen could be the reason he lost it.
Evade the Dark Empire storyline. Let Galen hunt after Carnor Jax or another Imperial/Sith figure. He can be outside-galaxy when 'difficult' storylines are in progress.
I'd love to see him fight at the Battle of Korriban though. Imagine fighting there, Jaden Korr running by, Luke and Kyle helping you out....
"I think the Devil ****s Dutchmen."