I would say the best way to handle it is to just not give the player a choice. Have your player pick it up, and "put it somewhere safe". It doesn't appear in the inventory, and the player pulls it out of their ass whenever it's required for the plot. Other rpgs do that all the time, it doesn't have to be a "omg, i can't throw this thing away" item, but as it is now, they've tried to give the players choices for every little thing, and written themselves into weird corners where SH just pops out of nowhere "tada!!!! box!", which is worse imo.
Definitely what I was thinking about when I said "stop trying to re-invent the wheel".
Just put this artefact at the end of the tutorial. The player take it because it looks important. Some characters are looking for it so our character understand more and more that it is important.
A few "permutations" are still eventually allowed - i.e you can give it to the gythianky but they try to kill you even if you gave them... so game over OR after the fight, they're dead and you take it back.
