Yea they don't have to remove classes, but they can rework the way future jobs work.

In the simple case of any class with the job system now they can just have 50+ be job only meaning SCH and SMN would not only level separately but they would also gain unique abilities for those 10 levels.

I would say a possibility in this would be guilds integrating the knowledge of jobs into their curriculum however with the current classes in the game this would only come to light after the lv job 50 quest of said job.