I have two shamans on the same realm and faction. It seems the settings are saved for my lvl 70 shaman and the game tries to load these settings for a lvl 32 shaman but it crashes since it cannot find the spells.

Mmh, in general it should work even if you have two shamans on the same realm.
I will have a look at it

They share the same profiles. In the config menu you can create different sets. For your lvl32 Shaman, you can create an other set.
With both Shaman you will have access to this sets and can share them.