How about this?
The "generalist" gets none of the fancy specialty-based benefits: he gets 1 additional casting slot of his highest level.
Or, if you wish to emphasize his broad study of magic: every even level (2, 4, 6, etc.) he adds 1 more spell to his book (perhaps every level, especially in...
There's a simple 5E rule about stacking: if it's not the same thing, it stacks.
I fail to see why all the fuss over this minor cleric option: the cleric that chooses to grant this benefit loses another option which may be useful in a different way, and quite possibly might be more fun to play...