Looking at the comp rules, these seem most relevant:
701.8a A spell or ability may instruct players to exchange something (for example, life totals or control of two permanents) as part of its resolution. When such a spell or ability resolves, if the
entire exchange can’t be completed, no part of the exchange occurs.
Example: If a spell attempts to exchange control of two target creatures but one of those creatures is destroyed before the spell resolves, the spell does nothing to the other creature.
112.7a Once activated or triggered, an ability exists on the stack independently of its source. Destruction or removal of the source after that time won’t affect the ability. Note that some abilities cause a source to do something (for example, “Prodigal Sorcerer deals 1 damage to target creature or player”) rather than the ability doing anything directly. In these cases, any activated or triggered ability that references information about the source because the effect needs to be divided checks that information when the ability is put onto the stack. Otherwise, it will check that information when it resolves. In both instances, if the source is no longer in the zone it’s expected to be in at that time, its last known information is used. The source can still perform the action even though it no longer exists.
Is the entire exchange ability countered because the Tree is dead by the time it resolves? Or do we use the "last known state" (toughness 0), thereby killing its controller?