I am not sure which three things you are referring to that Juan Tomas urges Kino to do. Juan Tomas is Kino's older brother and friend, and when Kino is in trouble, he goes to his brother for help and advice. When Kino first finds the pearl and determines to go to the pearl dealers to sell it, Juan Tomas warns him to be careful that they do not cheat him. He essentially tells his younger brother that the system is stacked against him, but Kino is determined to sell the pearl and reap the benefits of its worth. When Kino does not get a satisfactory offer from the pearl dealers in the village, he decides to go to town to sell his treasure. Juan Tomas gently warns against this action as well, telling his brother that "it is new ground (he is) walking on." Again, Kino does not listen to Juan Tomas, so intent is he on making his fortune off the pearl.
When Kino returns to Juan Tomas in desperation, after having killed a man who had tried to steal his pearl, Juan Tomas tells Kino that he should have sold the pearl even if he did not think the price was fair. Juan Tomas says, "there is a devil in this pearl," and he thinks Kino should get rid of it "to buy peace for (him)self." Kino feels that it is too late for that, however, so Juan Tomas urges him to hide in his house until he can make an escape. When it is safe for Kino to run, Juan Tomas gives him one last piece of advice, telling him to "avoid the shore," as that is where his enemies will be searching for him.
Leprosy is a disfiguring disease that was much dreaded in those times. Before the advent of antibiotics, it was highly contagious, and lepers were shunned from the communities in which they lived so that they would not spread their illness to others. When Kino, having nowhere else to turn, goes to his brother after he has killed a man, he says apologetically, "I do not want to bring danger to you...I know I am like a leprosy."
Kino is a wanted man, and by staying with his brother, he is putting him in danger at the hands of those who would wreak vengeance on him, Kino. Like a man with leprosy, Kino has the capability to infect all with whom he comes in contact with the devastation brought upon him by the pearl.