Autokrat
Considering that N was a soldier stuck on Malachor V, I would find it more likely that he didn't have access to magical gravity gun of which we have no proof exists.
Well how do you know that the magical gravity gun wasn't simply part of the standard Sith uniform, in case of emergencies?
Perhaps Nihilus is also some sort of MacGyver-esque figure and was capable of designing such a device?
I'm obviously teasing you about the gun, but there is no proof that has been offered that concludes that Nihilus tore the ship out of the gravity well through telekinesis.
You can say how it's the best possible explanation, but that doesn't make it absolute.
Autokrat
Although how he got it flying while stuck on the ground is a question.
If one removes the cartridge from the Magical Gravity Manipulation Gun and replaces it with a Repair Star Destroyer cartridge, it can theoretically be used to... repair a Star Destroyer.
Edit: RN's investigations concluded that the quote says "haul." But I'm not sure that makes a difference.