If it's repotting season, repotting is the best course of action. I try to remove all of the affected soil, usually dark areas that can smell bad. When I find dead roots, I cut back to healthy growth, even if it means cutting back to the base of the trunk. Leaving dead roots will let the rot continue. I leave the healthy roots alone.
After repotting, the tree can be dipped in a mixture of zerotol or a similar contact fungicide that's safe for the roots. About a month later I might use a systemic fungicide, though in general, proper repotting and using soils that don't retain too much water will usually take care of root rot.
If there's lots of rain, I'll keep trees in a sheltered spot so they can dry out between waterings. As much as possible, I want affected trees to get sunlight and warmth to stimulate healthy growth.