Yes, Crossrail will make getting to LHR easier from the Wharf. But it won't make LHR easier to use. Part of LCY's advantage is it is speedy to navigate (especially arrivals). I've got from touchdown to train in 9 minutes at LCY - that'll never happen at LHR.
A thriving city needs lots of transport infrastructure - and LCY is a very valuable part of that mix.