I believe the idiomatic way to use this library is to treat the tree as an immutable structure. When used this way, it supports the React Immutability Helpers, and the PureRenderMixin. If you treat it as immutable and use the PureRenderMixin, you won't run into the re-render multiple times issue described above.
See this issue for more details: https://github.com/Yomguithereal/baobab/pull/74