It's safe. The amount of material and its mass taht they are dealing with are so tiny and transient that none of the forces (eg strong force) they are studying are capable of interacting with the environment. Those forces are so tiny that they only affect things on a subatomic scale. For example, the force the article mentions holds neutrons and protons together. If something is farther away than a proton and neutron are in the nucleus of an atom (>1.75×10−15 m or so), it won't be affected. Maybe zorn will elaborate.
Yeah. The thing to keep in mind about the LHC, or any collider, is that they're colliding
particles, more or less one at a time.* And a particle is very, very, very, very small.

There are an
assload of particles in even the tiniest speck of dust. So even though the collisions can produce extremely hot "fireballs," and the particles move at extremely high energies compared with other particles, the actual amount of energy in a single particle or collision is still incredibly tiny by everyday standards.
At the LHC, the design goal is to get the particles up to 7 trillion "electron-volts." (Right now they're at half that, but the ion collisions they're currently doing make it larger.) That means the amount of energy an electron would have if you charged it up to 7,000,000,000,000 volts. (!) So that's a ton compared with the 120 or 240-volt electrons in your electric wiring, or the measly half electron-volt energy of the particles in an acetylene torch flame. But to put it another way: that's
ten billion times smaller than the energy stored in a single AA battery. So as far as safety, etc, the collisions and resulting fireballs are totally trivial... they're microscopic.
There's plenty of power at the LHC is though. The individual collisions are tiny, but the particle beams are not. Each beam has about the same energy (400 million Joules) as an aircraft carrier steaming along at ~10 mph or so, enough to melt a half-ton of copper. As you might guess this means the beams can be very, very damaging. The accelerator is located underground, so when the beam is "dumped" it is absorbed harmlessly by the earth. A screw-up controlling the beam could, though, potentially send it through some of the detectors or other equipment, frying some
extremely expensive stuff.
And the real awe-inspiring things are the superconducting magnets, which are what power & guide the particles in the accelerator. When the accelerator is running at full power, they contain a huge amount of energy in their magnetic fields --
the same amount of energy as a fully-loaded Boeing 747 cruising at full speed (almost 600 mph.) It's insane.
(The accident that knocked out the LHC for most of last year was related to the magnets. One of the electric connections to the magnets was not quite tight enough, and when it developed a tiny resistance the huge current through the magnet instantly fried it. The resulting "quench" of the magnet blew a hole in the cooling system and released two tons of helium; the pressure tumbled several of the 35-ton magnets off their supports.)
read more:
http://lhc-machine-outreach.web.cern.ch/lhc-machine-outreach/components/magnets.htm
http://lhc-machine-outreach.web.cern.ch/lhc-machine-outreach/beam.htm
http://blogs.uslhc.us/what-does-7-tev-mean