Make them immune to mystic mortar/mine, stands to reason. Not the skellywags though, they have related ability and come back as not completely gone anyway.
Maybe that's a special attribute saved to the forgotten Buccaneer, as no one seems to use them once they get the higher rated pirates.
I wouldn't want everyone to have that ability, but maybe a new ability to upgrade on the witch doctor. Once upgraded it added a - 1s stun to the skellies. Not making them immune, but having a shorter stun than normal troops.
Skellies have a reduced stun ability don't they. If resurrected troops not stunned are too powerful then could nerfing hit points a bit. They do very little damage anyway.