Not only can't the LHC produce non-significant amounts of isotopes, it cannot produce any isotopes. Hadrons = heavy particles, e.g. protons and neutrons (vs. Leptons = light particles, e.g. electrons).
They collide protons at speeds near the speed of light. Which collisions produce a number of other elementary particles - but no isotopes (actual atoms). It is just on another (smaller) scale.
Whatever nefarious plans this guy had, they had nothing to do with CERN as such. Unless he planned to sabotage the LHC, which would be costly but non-destructive beyond that.
You can make new elements by proton bombardment, I watched them make PET scan isotopes at UC Davis Synchro Cyclotron.
But those were only 60 MeV protons, and the target was in the beam directly. For my own work I used ultrapure aluminum as a dosimeter, looking for Na24 produced by spallation followed by alpha emission.
You are right, when a supercollider is running properly the only target is hadrons. Run the beam into a beam dump, though, and you’ll get activation.
The collisions will produce neutrons and other baryons, which can activate anything it hits, but on a mass basis that will be relatively small and impossible to collect in a jar.
I was at part of RHIC (the heavy ion feed line after the Tandem van de Graaf) and there were activated components there.