my 2 cents on this matter is this
1. don't remove the classes, make it so the DoW&DoM classes cannot level beyond somewhere around level 34(this is the max sync level for the final class quest and the first job quest)
2. put in clearer instructions how to get your job at the class NPC when you turn in your final class quest(even if this involves having the Job NPC appear)
3. make the job stones consumables, once they are consumed the job can nolonger be reverted to the class(make it so the SMN and SCH stones can be consumed by either the ACN or the other job)

to me having it changed in this way would help in lots of ways