You get to choose between Joja and the CC again during each farm/playthrough, so that's not an issue.
I can understand not wanting to lose your progress, but starting a new farm is actually really refreshing once your "main" farm hits seven year or so. Definitely pick a new map, use the knowledge you've gained to do everything faster and more efficiently than the first time, and don't forget you can just skip cut scenes if you like (minus button on switch, not sure how on other platforms)