You might find a moral dilemma between the MC and the OS throughlines. For example, the MC "player" having to choose between something to do with her personal issues and pursuing the Goal. (At its most climactic this choice could mean Failure if they don't pursue the Goal, but it doesn't have to.)
In that case, where the dilemma is in the intersection of the MC and OS, the Critical Flaw is a great place to look, as you suggested.
Perhaps you can also find something in the MC Resolve, since Change is never easy, nor is remaining Steadfast under pressure to change.
More generally, I think you could find fodder for moral dilemmas in almost any Dramatica story point. A moral dilemma is a way of taking the story point / gist and making it into a real source of conflict. Imagine the writers of The Fugitive were Dramatica users: "Hmm, OS Problem of Help, something about a kid needing help because the ER doctor diagnosed her wrong... But to make that a real problem we need to have it so Dr. Kimble would need to put himself and his whole mission in jeopardy by saving her..." Not that he agonized over that dilemma, but you can see it working.
But though you might get ideas from one story point, I think a moral dilemma would tend to be "multi-appreciation". That example of the misdiagnosed kid hits on OS Problem vs. MC Problem and MC Critical Flaw, for example.
If you wanted to make it even bigger, you could bring the IC and/or RS throughline in. Maybe the IC is influencing the MC to change perspective and help achieve OS Goal, and there is relationship stuff bound up in there too, but the MC resists the change. Now that's a climax!