It is easy to understand why Juan Tomas shields Kino after he kills a man. Kino is Tomas's younger brother and he feels it his duty to protect him. He knows that Kino has made many enemies over the pearl. People are envious and have tried to steal it - although Kino does not help his own cause much by being proud and unyielding over its possession.
Technically Juan Tomas may be in the wrong for shielding a killer, but on another level he is correct to do what he can for his close kin. Kino, after all, killed the man in self-defence, and is most unlikely to get a fair hearing as the community has now turned against him. It is no surprise if Juan Tomas feels that the best course is to aid and abet Kino's escape.
Although he helps him, Juan Tomas also realises the danger that the pearl has put Kino in and counsels him to give it up:
There is a devil in this pearl. You should have sold it and passed on the devil. Perhaps you can still sell it and buy peace for yourself. (chapter 5)
Tomas speaks of the pearl in somewhat superstitious terms here, with reference to the 'devil', but the very real danger from it, in the shape of envy and hostility from others, has already been proved. However Kino refuses to listen to his older and wiser brother and holds on to the pearl even when he is being forced to flee.