in addition to #1 and #2 in the OP I think there are 2 other options that could work (I'll use paladin example):
3 - Paladin is a distinct class with completely unique abilities. PLD offers like 50%-70% affinity with GLA and CON by default (assuming default is 0% or something).

4 - Paladin is a distinct class with overlapping abilities to GLA and CON plus some unique abilities (so PLD would unlock Cure II later than CON would but it retains full affinity for the ability).

Either way I'd make there be a pre-req to unlocking PLD like leveling GLA and CON to 20 and completing a quest or something.

Anyway, good thread with lots of good ideas.