As soon as you start to cast Scourge of Nel Toth from your graveyard, it moves to the stack. At that point, it’s too late for an opponent to prevent you from casting it by removing it from your graveyard. It’s also too late for players to try to destroy the creatures you sacrifice to pay for the spell.

If you cast Scourge of Nel Toth from your graveyard, it is a spell and can be countered.

Casting Scourge of Nel Toth from your graveyard by paying the alternative cost doesn’t change when you can cast it. You can cast it only at the normal time you could cast a creature spell.