It is currently not possible to deconstruct raft bases. When attempting to deconstruct bases players will receive an error message saying the object still supports other items and cannot be destroyed.
Update: This issue may not affect every player, some players may find they can deconstruct bases without issue. If you have found this to be an issue however, please let us know.
There is currently no workaround for this issue. However, it may be possible to break down raft bases if only one side is attached to something else.
Note: User TwistedShadowSaf found that when trying to deconstruct some parts of their base, that flipping the base upside down allowed them to disassemble parts of their raft. If you try this and it works for you, please let me know.