Taking INTO DARKNESS into consideration the size of 350 meters is about right.
Several hints at that: Kirk and McCoy dive to the Enterprise.
A bigger issue that relates to a smaller ship size concerns this "dive". First, the E has to be sufficiently under the surface to remain hidden. Let's say it's only 30m down. A 350m ship is about 100m tall. A 750m ship is over 200m tall. As I recall from the 10min preview (haven't seen the movie yet), Kirk and Bones swim down to the secondary hull hatch to enter. That means they dive either about 100m, or they dive 200m.
Both are ridiculous when you consider pressure effects (but hey, maybe they have a widget for that), but one is much less
ridiculous than the other....