It's been moral value all along. What is morally valuable (or rather what is the measure of moral value) is persons' ability to understand and make their own choices. It isn't about whether you value your ability to do so or not, or whether that provides some value to your life, the claim is that the extent to which that ability is violated or restricted determines the goodness or badness of the consequences of some action (and therefore the morality of that action).
No, there isn't a contradiction there at all. It's the ability to understand and make some decisions that ought to be protected, but not the ability to understand and make others. That is entirely coherent.
Again, you are getting caught up in things being valuable "to" people. What I am claiming is that the ability of persons to understand and make their own choices is the measure of moral value. The thing which makes the consequences of an action good or bad. It is not about what is valued by people, it is about what matters morally, objectively, universally, whether or not we care about it.
I'm going to draw a comparison with two other types of consequentialist theory so that it is really clear what role the ability of persons to understand and make their own choices is playing in freedom consequentialism.
In preference utilitarianism, the measure of moral value is the satisfaction of preferences and the lack of dissatisfaction of preferences. This is what is what determines the moral value of consequences, their utility. Now, if a preference utilitarian had to choose between five people losing their sight and one person losing their life, then the right thing to do (according to their theory) is whichever satisfies the most preferences/dissatisfies the least. It doesn't matter if the preference utilitarian doesn't have a preference for either one occuring, because the people who are going to lose their sight and/or life sure do, and their preferences matter morally.
In classical utilitarianism, the measure of moral value is happiness and the lack of unhappiness (or pleasure and the lack of pain if you prefer). This is what determines the moral value of consequences, their utility. Now, if a classical utilitarian had to choose between five people losing their sight and one person losing their life, then the right thing to do (according to their theory) is whichever leads to the greatest overall happiness minus unhappiness. It doesn't matter that the person in question is made neither happy or unhappy by making the decision, because the people who are going to lose their sight or lives are going to be made happy/unhappy by it, and their happiness/unhappiness matters morally.
In freedom consequentialism, the measure of moral value is the ability of persons to understand and make their own choices. This is what determines the moral value of consequences. Now, if a freedom consequentialist had to choose between five people losing their sight and one person losing their life, then the right thing to do is whichever protects the most freedom (or perhaps the most important freedom? This is very much the problem that I haven't solved yet. How to weigh freedom over different things in such a way). It doesn't matter that the choice in question doesn't require protecting, because the choices of the people not to lose their sight or lives do, and their ability to understand and make their own choices matters morally.
Does that clear things up?