The spots look to me like Apple Cedar Rust.  Over east, where I’m at, I’ve witnessed it on my young apple trees.  I’d ignore it, and do. If it is ACR, I don’t believe there’s much to keep the leaves blemish free.   

The pruning question's easy  ‘tip pinch’ the terminal leaves off the small competing shoot.  Let it’s remaining leaves feed the tree this season, then prune it flush with the trunk next spring.