"Discipline is freedom" summarizes the attitude that if you have trained yourself to wake up early, stay on task, exercise regularly, etc., etc., then you now have the freedom to do a variety of things that you would not otherwise be able to do. By having the discipline to exercise, you now have the ability to freely use a more fit body, by waking up early, you have extra hours at your disposal, and so on.

To address your first question, I think Jocko would probably say: "If you form an intention to do something, and you don't do it, then you are mentally weak. The first thing to do is then to decide not to be mentally weak."

In abstruse lesswrongspeak, this would like something like: "It is most important to form a self-governing narrative of the form 'a mentally strong person would execute on their intentions regardless of transient impulses or mental resistance, and I commit with utmost resolution to being a mentally strong person'. Then you must continuously monitor your daily activities for adherence to this commitment and to this narrative-mentality."

Ironically, the Less Wrong deconstructionist approach of breaking the self up into multiple agents and carefully finding a minimum-enthalpy path through wantspace is itself antithetical to forming such a "simplistic" self-governing narrative, even if possessing and maintaining such a narrative were more effective.