The Port Broughton article seems rather open, indeed but from the entry from Joan's, I certainly got the impression that Midway is still alive and still the flagship:
"The famed Midway-class formed the nucleus of Earth's wartime defense, with the Midway herself at the head of the fleet. Modified and improved over the past twenty years, the current Midway-class ships differ only visually from the Confederation flagship."
It the Midway would be destroyed, I guess it should read "former Confederation flagship" or so. Still, no big deal if they actually want to have the Midway be destroyed.
But in skipping through the manual (God, it's such a great manual, awesome, awesome, awesome!), I stumbled upon something which I don't think is worth a new thread since the answer I gues is "we don't know", so here it is:
In the Port Broughton article, on page 51, right on the top it reads "...displaying the first ten Midways." I guess that means that more Midways were built or are at least planned.