I asked Islington Planning Officers for their observations on the removal of access from the East side of the station and how their views would be raised with Camden. Their anonymised response is below.  I still think that the answer here is gated/ticketed access barriers in two underpasses dug under the new track emerging on the current platform one inside the station and on both the east and west york way pavements of york way.  the underpasses could have shops in to keep them from the fate of normal underpasses:
Islington panning officials response is in the document at the link below

Download from_islington_planners.doc