1. Protons, aka ionized Hydrogen, is an abundant element here on Earth and the universe in general. Hydrogen's relatively low mass makes it easier to manipulate (using electromagnetic fields, in this instance) than something heavier, such as Helium, Lead, whatever. The LHC primarily targets creating as many high energy collision "events" as possible, so Hydrogen was chosen. With larger ions, you do have a larger effective collision cross-section area (larger nuclei), but it's a diminishing returns kinda thing: Helium weighs four times as much, but only produces around twice as much cross section. RHIC at Brookhaven still does some heavy ion stuff to this day, but they're not as focused on pioneering higher energy collisions as the LHC/CERN.

2. Really, it's a facility integrity/costs/schedule kinda thing. It's not so much loss of human life or the "black hole boogeyman" as it is protecting sensitive equipment that you could ruin if you're not careful; In this case, the superconducting magnets that need to be cooled via cryo pump to ridiculously cold temperatures, -270C or cooler. Anytime you're working with cryo pumps, things just get way more complicated. And badass. Just don't want this to happen too many times.