You aren't as safe as you think
Other properties of the ship
The combustion chamber need not be made of any sort of imagined material. Conditions in today's rocket nozzles readily exceed the material properties of the nozzle, so measures are taken to protect them. Cooling is the biggest, some use the cryogenic fuels through the nozzles as a preheat, others use a stream of fuel to form a layer between the combustion and the nozzle.
The same could be done with the nuclear fire of a torch ship. The plasma in a test fusion reactor is contained in powerful magnetic fields and kept away from the walls of the container. The same could be done with the torch ship, stand off the reaction from the walls of the chamber, add some radiation shielding and a cooling system and you are all set.
Beam Weapons (To include directed energy)
A beam of charged particles could easily wreak havoc on the nuclear reaction, admittedly it would be challenging to ram through the exhaust stream, but focused enough and it could get through. Adding alpha partilces to a fusion reaction could snuff it out or cause a runaway reaction. Beta Particles could cause issues as well by changing the charge of the plasma. The effectiveness of this depends on the magnitude of the magnetic containment and its polarization. A beam of neutrons could also cause issues, interfering with the reaction and adding a ton of extra energy to the chamber as they decay. Heavier Ions will also interfere with the reaction and do physical damage to the containment chamber.
Pick your wavlength of the laser, and dump plenty of power into it. Depending on the content of the reaction some wavelengths may pass right through it and damage the walls of containment. I'm thinking gamma radion of a magnitude that exceeds the design of the torch ship. Likewise, some wavelengths may be absorbed by the reaction and exceed the design of the ship, I'd guess microwaves. Results may vary, ask your lead engineer if you have questions
Relevant XKCD Comic.
Moving fast enough and your kinetic projectile will be unaffected by the nuclear fire. If the contact with the heat is brief then the projectile won't have time to vaporize/ablate away. I'll see if I can apply some thermodynamics to it later on. Also, even if you manage to vaporize it, now you've got a cloud of vapor with the energy of the projectile moving towards you.
Getting them into the chamber is the main issue. Get through the exhaust stream and your payload will do its job.