Yeah, Canada Water is frankly near breaking point in the morning peaks at the moment. The Northbound Overground platform has one escalator down to the Jubilee Line and it's congestion regularly skirts 'dangerous' IMHO. While there's a large waiting area away from the platform edge for people wishing to use it, it's now barely emptying before the next Northbound overground pulls in. At 20tph I don't think it will cope.
But you're right, Crossrail may be the saviour. Although it seems unlikely many will wait to change at Whitechapel to get to Canary Wharf (unless their office is at North Quay i.e. just outside the Crossrail station), those going to Stratford may well change their journeys. Westbound, a lot of passengers who get on the Jubilee Line at Canada Water seem to stay on well past Waterloo (my old commute, I remember the patterns). So hopefully this means Crossrail will present a higher capacity, quicker westward link for many of their journeys too, wherever they might be going eventually, staying on the Overground until Whitechapel might attract a good fraction of them.
If there is not a wholesale switch, the only alternative for Canada Water would seem to be a very awkward one way system in the peaks.
The awkward 1way system has been used at times before. The single escalator was some what due to fears about the Jubilee platforms getting too crowded (original frequencies) combined with cost minimisation.
CR impact: We're looking at 15-21 months till the initial 12tph Abbey Wood - Paddington service on CR which may not be enough to get people switching initially due to comparatively low frequency and capacity.
TfL could of course uncancel the next phase of Jubilee improvements... I suspect one of the reason they could justify it was Jubilee growth expected to flat line for a number of years post CR opening.
Overall just 10-15% of the Canada Water changers swapping to Whitechapel would make a big difference.