I can't agree with the idea of diverting all the DC lines service away from either the traditional terminus or a new cross London route (e.g. Crossrail).
In respect to freight interaction and future potential HS 1/2/ transfer traffic, I refer you to my idea for diverting NLL and GOBLIN to Kentish Town to avoid significant work at Camden and improve connections. This gives both LO lines a new interchange with the Northern Line and the Thameslink MML arm.
http://www.townend.me/files/kentishtown.pdf
At Stratford a fair proportion of the freight traffic is continuing on down the GEML to Felixstowe. With double headed electrics and maximum speed of 75 MPH, this traffic fits much better on the main (fast) lines, does not have to cross to the reliefs and is thus not affected by Crossrail developments.