The ship going into the water isn't the Enterprise, the warp nacelles are too far apart.
We've proven at STL the one coming out of the water is the Enterprise, or at least another ship of the same class.
As for the bad guy?
The IDW comics are said to be canon in the New Timeline. So...Gary Mitchell is dead.
Khan wasn't in Starfleet. The threat is said to be "from within."
Charlie Evans wasn't in Starfleet either.
Cumberbatch is Garth of Izar. Garth was a brilliant starship captain who went insane and decided he wanted to rule the universe. Watch "Whom Gods Destroy" again...it fits.
The only other Starfleet officer of note who went insane in TOS was Ron Tracy.