First, I would say that the Samara you summoned could not cast a Seedling Pod that turn, since during the Deployment Phase you can only cast the spells you've chosen during the Planning Phase. During the Planning Phase, Samara Tree was not on the field, so you could not select a spell for Samara Tree to cast during the Deployment Phase.
Onto the other question.
Text on Seedling Pod:
"During the Deployment Phase, if there is 3 or more mana on Seedling Pod, it may cast 1 plant creature or conjuration which targets its zone, an object in its zone, or a border of its zone. If it does, destroy Seedling Pod."
So based on that, the trigger to destroy Seedling Pod happens right after Step 1 of casting a spell. I think the player with initiative would be able to decide which happened first: Step 2 or destroying the pod. I don't think it would make much difference either way though since Seedling Pod would be destroyed because Step 3 was completed (bring Samara Tree out and giving Seedling Pod Cantrip).
Unless of course the player with initiative could reorder destroying the Pod and Step 3, in which case the Pod would return (provided you had initiative; I don't think an opponent would let you get it back). I don't think it would be worth it though, since Samara wouldn't give you a new Seedling Pod.