I thought we've played it so that the negative level is on a 'per casting' basis. So, a magic missile spell with 5 magic missiles, if all of the missiles hit one target, that target still only loses 1 level. However, if the 5 missiles each target a separate foe, then all foes hit by the missiles lose a level. In each case, only 1 level is lost per target because the damage results from a single casting
The same way that if you cast a Fell Dell Drain Acid Arrow. The damage from the spell persists for multiple rounds, but the target only loses 1 level, because the resulting damage is from a single casting of a spell.