First: Shameless Plug
Now on to the blog.
It's hard to devise ways to hurt a being without a body. If you're going to interact with Non-Biological Entities you face the prospect of facing one you or someone else has pissed off. No one wants that. Even if they aren't pissed off an escaped NBE may not want to return to the engine willingly leaving you stranded 100 A.U.s from the nearest rock.
Of course most players will fall back on Liaison, Carousing and other social skills to persuade the entities it's in their best interests to return to work. They will deal with them in an enlightened and fair way and these beings will certainly adopt a reasonable bargaining stance.
So how do you make a ghost get back to work? It doesn't bleed so you can't shoot it. It doesn't exist to most sensors for gosh sake. They have minds and some form or awareness. This is based on some form of exotic matter having a structure. This the way a person with Education 13 says, "Damned if I know!"
Some groups will attempt to strike a deal ("Okay we'll get you episodes of this show 'The Golden Girls' from the Dark Ages. Now take us to a stable orbit!") Many will not and may not even have that option.
The first best response to an angry NBE is a skilled psionic who can perform psionic assault. Psionic assault reduces the NBE's psionic strength by the damage rolled. Of course sometimes the NBE beats the psionic to the draw. Even if the human does draw blood so to speak it may not have put down the NBE and even with psionic boosters Assault will drain a psi pretty fast. Unless you have more than one psionic on the ship assault probably won't finish off the NBE by itself.
After or even before your psionic makes their move there are several ways to weaken an NBE. Only a madman fires plasma weapons in a ship. More controlled procedures are necessary. The NBE's create cold spots as they work their psi by absorbing heat and electrical energy to power themselves. The power to a section of ship containing the entities can be cut off. The drives are already sealed off by design. A corridor or compartment can be powered down. This can often make Haunts and some Overt entities go back to the energy rich containment fields of the drives for sustenance.
More willful entities can be de-powered by using endothermic grenades. These cost and are otherwise identical to fragmentation grenades. When they go off they chill a 3m by 3m area of deck causing any NBE in it to lose 1d3 psionic strength.
Some organic materials serve as a 'spirit repellent' for unknown reasons. A sub pistol loaded with the proper chemical mixture can also cause a NBE to lose 1d6 psionic strength. It is identical to gas rounds but the only affect on a human is disgust at the awful smell.
Psionic shield technology can be used to contain NBEs. For that matter they can emit a weak form of psionic attack (2d6-4). Such jury rigging is undependable at best. Hucksters also sell a variety of ghost stunners with no proof of effectiveness. If it doesn't work most customers won't show up for a refund ...
Or maybe they will. You just won't see them.