Protons that could cause controlled visual hallucinations in people. If they can cause that level of interference with our nervous system, they can kill us. Even if they were somehow limited to visual hallucinations, a well timed hallucination is easily lethal. They probably ought to be able to hack into computer systems with that as well.

Tbf, from the way they were described it should have been fairly easy to defeat the Sophons even without any science-fiction technology; just build e.g. 10-20 particle accelerators distributed over the world and take measurements close enough in time to each other that you cannot be at multiple sites without exceeding the speed of light. Then at most 3 of them could be corrupted for any given run, and these can be thrown out as statistical noise.

I think the argument was that they could send Sophons faster than we can build particle accelerators.

This is addressed in the book; a new sophon is cheaper than a new particle accelerator.