Healing the tree is a losing battle since the spawns do way more damage to it than you can cure the tree for.
Best bet is to go on the attack as quickly as possible. Try to use Aero to run and grab hate on the invaders as soon as they appear, and gather as many as you can to one spot and Holy them to death, then pick off any stragglers.
+1 on Stoneskin for the Tree, great for Chocobos as well.
I holy'd the easy mobs early, to give me room to not waste Shroud of Saints MP returns, and to get it's timer ticking for round 2 quickly. Wipe out each round as fast as possible, spam heal the tree in the lull, use divine seal, Regen, restore Stoneskin if MP isn't too abused. I can't remember in the blur if I used Repose at all.
Elixirs are dirt cheap lately, 6 minute cooldown, but good returns on Mp for a single shot.
Good luck, only took me 2 tries, first time I kept healing the NPC's and the tree died horribly. It's a workout of all your skills.
Like other posters said it use stoneskin on the tree, this helps a lot. What i did was basicly holy the first adds that come, close to the tree. Cure the tree the couple of seconds you have before second pack comes. Kill the bees asap and from distance. They die really quick i believe a normal earo would kill them after a few ticks but not 100% sure about that since it is already been a while since i did that fight.