Not destroyed but shifted considerably-the collapse of the RSE would affect the astropolitics of the alpha quadrant greatly.
It could presage war with the Typhon Pact or lead to the remnants of the RSE being absorbed into the federation.
Also the disappearance of Spock should have an affect on the living characters who knew him.
As enterprise and voyager show us-the federation is alive and well by the turn of the fourth millennium with time ships and time cops-the DTI novellas have expanded on this further-what I want to know is how the federation gets to this point-or if not that at least a general idea of the path the next five centuries IU will take to get to that point.