That's not necessarily the case. The primary imbalancing factor is stats and not skills. Level 15 skills at level 80 stats are stronger than level 80 skills at level 15 stats.
All that's needed to balance high level skills is a damage/healer multplier, which the game already has plenty of (weakness, damage down, etc). The value would change for every level but SE already knows roughly what the value is needed at each level because SE has been able to balance boss health for the entire game.
If you're worried about special effect skills (example Benediction) then just give them sync traits, so for example a WHM below level 50 only gets 50% heal (or whatever number) out of Bene.