Uhmm!
When my opponent was about to activate Necrovalley to protect it, I countered with a trap to destroy this monster... he was still on the field...
It's face-up on the field already. (Hence why you can chain a card like Cosmic Cyclone to a Field Spell and banish it.) It doesn't need to resolve to... Exist.
I think your problem here is that Supernaturalist doesn't require Necrovalley to be activated. Instead it just requires Necrovalley to be face-up on the field.
If there is a card that can permanently negate a field spell without removing it from the field Supernaturalist would still don't care.
No, Spells/Traps in the Spell/Trap Zone work the same way. For example, if a targeting effect is chained to the activation of an Equip Spell, you can send that Equip Spell to the Graveyard to activate Red-Eyes Slash Dragon's effect even though it hasn't resolved yet.