This seems t be a good opportunity to use a disease track. You might modify the Endurance and Heal checks to represent something or a magical nature (Charisma and Religion checks?)
I get you Uller, but the point is to give the players informed choices. To let them have access to the information that it can be destroyed... but not easily. Then they can willingly take on the consequences of its destruction.
There's a subtle difference between players destroying an item, and bam, a punishment... and players destroying an item KNOWING there's a punishment. The first is a DM lesson. The second is a player choice.
The latter is the fun one.
I'd even encourage a 'You might, in fact, be cursed.' as an ender for it... roll some dice in secret... and then let it go. Let them THINK he might be cursed, and unsure as to why. Role stuff against that character behind the screen. Make him sweat.
Game mechanic effects: None.
Psychological effects: Priceless.
The good news is, now that the PCs have narrowly escaped a debilitating curse of DOOM, they are informed for future bouts of item destruction. I don't have to have an evil shadowy skull spirit try to eat me more than once to figure out I should consult an oracle or something next time I try to break a mcguffin.
So now they know the skull is being sought by the necromancer to help him control/create undead using the rift he is opening. They know there are other similar skulls buried in the burial site, so they decided to just destroy it.