I have a 5' Sambo (Sweet) lemon tree. Basically, I happy with the shape and don't want to do anything to it.

From the top main stem of the plant, there is this one small branch that sticks out about 12" that really doesn't amount to anything. It has maybe four leaves on it, and no signs of blooms. It ruins the shape of the tree.

I am sure I can cut it back. The question is do I use a sealer on it after I do, or leave it alone?

spray with lysol that contains at least 59% alcohol or simply dab with cotton dipped in 70% rubbing alcohol your pruning tool and around where you want to cut that branch before and after. Sealer will just seal in the pathogens if they happen to land when you cut them.