I think that is the implication from the pilot actually, that Mercer was always a really good captain who just became dispirited when his marriage fell apart. Now, we get a chance to see what the pilot was alluding to.
Now we have to wait for what happens when he finds out Kelly made this command possible. Regardless of her motives, he's going to be crushed, pissed, etc. I wonder if this is something they even plan to do in S1, possibly after more thawing between Ed and Kelly.