Cruise Missile
I suspect that the only real way to make this work is by having players fly a "missile" that has no shield and an explosive Fuse. I'm pretty sure that there aren't any other ways to do this- FL doesn't seem to offer "Missile View" like many games of this kind do, let alone give you control.
Probe
I'm pretty sure if you attach a sensor to a missile, it won't work. But what about attaching weapons to a missile, with auto-turret enabled?
Weapon Disrupter
Well, first off, such a thing is
already in FL. Any weapon that does Energy damage will suck Energy out've ships once their Shields are down. I dunno why most players don't get how important that design choice was...
Secondly... you could basically do this with Missiles... but the disruption would be permanent (heh). You could give weapons low hitpoints, and then have Missiles that had wide area effects but low damage. So if people lost Shields and then got hit... voila... they're disarmed. Which could be very funny in PvP
Engine Disrupter
Well, you could do a varient on the whole Weapon disruptor thing, above... but ... I'm not sure the FL game engine would be happy if a Ship lost its Engine.
Jumpgate Disrupter
I dunno why nobody seems to have investigated what the TLR_shield does, but it might be worth a shot. At any rate, you can give things a Fuse that makes them appear to be destroyed pretty easily. Or just use a different CMP/SUR that might make it more practical to defend the Jumpgates. Or...
Basically this one has to get solved indirectly, I think. Unless TLR_Shield works. I don't have time to investigate that right now, nor to get into serious detail- you need to go investigate the Trade Lane Rings, which have some funny Hardpoints, funny scripting, and funny equipment. I'm pretty sure that some of that stuff will have interesting and useful effects elsewhere.
Disrupter Field Generator
This one's super-easy. Just make a Missile that has a gigantic detection radius, set it up as a totally harmless Cruise disruptor that just knocks out Cruise, and then attach it to a ship. Player fires Missile, Missile detects Player's ship (yes, players can set off their own missiles) or anything else in the area... goes off... no more Cruise.
The problem here is that such a thing will very likely cause massive lag in MP.
”Ghost“ Ships
Set phantom_physics = true. I see no reason why this couldn't apply to ships as well as Solars, but I've never tried it. This sort've thing is controlled by the server, not the client, I think, so it's useless as a cheat.
Don't mess about with the SUR, or the ship will not render properly.