If you trigger Tree of Perdition's ability, then give the tree -13/-13, does the player go to 0 life?
No - the Tree's ability will fail to do anything when it resolves. After the -13/-13 effect resolves, the Tree will die as a state-based action. Thus by the time the Tree's ability resolves, it won't be in play so the exchange can't happen.

The general rule:


  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.


And confirming this, a specific ruling for a very similar card:


  If Tree of Redemption isn’t on the battlefield when the ability resolves, the exchange can’t happen and the ability will have no effect.