Marshall is going feral, and even though he sincerely converted to Mormonism the conservative Mormons, lead by Bishop Mordecai, still pressured Jeremiah into forcing Marshall to the outskirts of the community. Apostle Jude has volunteered to tend to Marshall despite the increasing radiation doses that will eventually overwhelm him, resulting in his death.
Deal with Marshall: Bishop Mordecai and Doc Angela are concerned with Apostle Jude's visits to Marshall. Mordecai wants Marshall to leave New Canaan, Angela just wants Marshall to stop contact with normals until he dies or gets radiation treatment. Though Marshall has difficulty communicating it, he really just wants to go out into the desert to die far away from everyone else.
Kicking Marshall out of New Canaan and/or killing him is intolerant and somewhat cruel, and results in a small amount of negative Karma because Marshall doesn't want to die, he just doesn't want to hurt anyone.
If Marshall is just left, Jude will develop cancer from repeated exposure to radiation and die. Marshall will lose his mind and wander off and die by a house, the two residents will die of acute radiation sickness by absorbing it through the walls.