You can prune citrus almost any way that pleases you; but the danger of pruning lower limbs is in your climate, if you expose the trunk to the sun, it can sunburn and kill the tree. If you decide to prune it up, I would advise painting the trunk to protect it; cheap white latex paint thinned 1 to 1 with water works well.

Thank you, we'll do that.

Will we harm the tree if the lower branches are pruned off when the tree is tall and more mature?

Nope

If the tree is mature with a wide enough canopy, as John mentioned, all should be well. My brother has a very old Navel orange in his backyard, and it was poorly pruned last Summer. Still, it's doing alright.

Josh

Thank you! Nice tree, and beautiful yard.