In many articles i see that the explanation for the College of Winterhold seemingly untouched is that it's unknown as to why its still up and why it's untouched.
So my theory is that the Midden, the big underground dungoen to the College kept the College up and why the giant rock in which the College rests upon is untouched by the waves. Also inside the Midden theres the Auger of Dunlain, Draugrs and Ice Wraiths which makes clear knowledge that in the Midden also holds alot of magic. The Midden also is built very sturdily and is made very tough so i think this is the most likely reason as to why the College still stands.