Mtg creature spells, instants, priority?
Your Ghoultree will still resolve fine; your opponent can’t prevent it by exiling cards from your graveyard after you have cast Ghoultree. 

The casting cost of a spell only matters when you are casting it. You declare your spell, put it on the stack, pay it’s costs; and only then does your opponent have a chance to respond. 

Your opponent could have cast his instant earlier; before your main phase, but he would have had to know that you were planning to cast Ghoultree. There is no time between you declaring you are casting Ghoultree and you paying the cost where your opponent can act.