Good morning Rebecca,
Your post raises some interesting questions about our relationship with the natural world. By pruning the tree you are, in a sense, helping the tree and in nature itself, high winds, storms and fires also “prune” trees. On the other hand, you have written that you want to prune the older boughs to divert energy into the younger ones. Is this your decision to make? Perhaps you should spend some time meditating with your tree in order to decide – together.
As far as respecting your tree, why not wassail your tree with elderflower or elderberry wine? That’s an old country tradition, usually for apples and pears, but I see no reason why any fruit bearing tree couldn’t be honoured in the same way.
In Celtic beliefs, the elder tree is a fairy tree, so work carefully with it and establish a good relationship and you will be establishing a good relationship with the fair folk.