I don't think GMs will fiddle with people's inventories to that degree, given that you're limited to one item restoration over the entire lifetime of your account – and I wouldn't try spending that restore on getting rid of something you can't reclaim, even if they were willing to delete it for you.

The soul crystal section of the armoury chest has space for all jobs, so you won't run out.

Also, if this is about not wanting the jobs linked to your character, I don't think that has anything to do with owning the crystals themselves, since the underlying classes don't need crystals so I don't think they're connected in that way.