I would at least put in some mechanism that allows a Spells Known caster to replace the spell with a different spell at some point during later downtime. Or allow the loss of the spell to be cured by some kind of powerful restorative magic of some sort. Something to make recovery possible, but impractical in the moment that they have stolen it.
There is no precedent for such complete and irrevocable destruction of character abilities, and I do not think there is a good cause to arbitrarily penalize anyone playing a Spells Known caster for their choice of class.
I get the fluff is important. Disable their access to that spell, because it was stolen, sure. But let them get the Spell Known Slot (at least) back somehow.