The notorious Ghost Die of the Ghostbusters role-playing game is a wondrous thing. It is, perhaps, the earliest known example of a "wild die," meaning a die that is rolled with another die or a dice pool to introduce the chance that a result may be drastically influenced in a harmful or helpful way. From the Ghostbuster's point of view, the Ghost Die is never helpful. It complicates success, it exacerbates failure, and it rewards foes.
As I've mentioned previously, coming up with entertaining consequences every time a Ghost is rolled can be taxing on one's imagination and may even slow down the game. When rolling a Ghost becomes a nuisance rather than a novelty, it's time to reassess the role of the roll, if you will.
My solution is the discretionary Ghost Die. Don't include it in every roll. Roll the Ghost Die only when a ghost or any other supernatural phenomenon is involved. When Ghostbusters are knocking on the door of the spirit realm, that's when it's time to let the Ghost Die build tension. As per the rules, when a ghost rolls a Ghost, it benefits the ghost. When a Ghostbuster rolls a Ghost, it still benefits the ghost, regardless of whether the Ghostbuster's roll is a success or failure.
Furthermore, don't treat it as a D6. The discretionary Ghost Die is only rolled when the paranormal is encountered, so treat all faces except the Ghost as blank. It's an extra die used as a special effect it is not part of the dice pool.
The best part is that the Ghostmaster only needs to worry about the ramifications of rolling a Ghost when there's a ghost to make it easy.