I assume you mean secundus, right?
They come from the Latin root sequi, meaning 'to follow'. Unfortunately the OED and etymonline.com are not very helpful; the Latin secundus could mean 'assisting, favorable, following, second', and they don't provide any explanation of the differentiation of senses in Latin. I'd have to guess something along the lines of what you've said—that a second is someone who follows and assists, which makes them favored or favorable. Other than that, I got nothin'.