Some species of urchins, like your pencil urchin are not sharp, making it no threat to you by being stung or getting an infection. The Black Diadema Urchin, in my opinion, is the best urchin for a reef because it is not cumbersome and won't knock over corals and rock. You can pick these up carefully. Then their are other urchins that will sting you causing a rash, itching sensation or even a slight pain. Then their are the Fire Urchins, that should be not opicked up at all since they possess venom!
You should always try to reduce the time and likeliness of having your animal remaining out of water.