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.
I always figured the reason C'baoth had no lightsaber was because he didn't need it.
"There is something going on in time and space, and beyond time and space, which, whether we like it or not, spells duty." -Winston Churchill
"For of all sad words of tongue or pen, The saddest are these: 'It might have been!'" -John Whittier
"Apathy is death." -Kreia