It seems a current trendy thing to remove convenient conflict-free pedestrian routes, I think anything with steps (like the north side of the York Road footbridge) is seen as fair game, because if you can't get a wheelchair down it then nobody is going to have it. This extends to demolishing what were quite expensive to build and convenient facilities, like this one.
The underpass outside Tower Gateway DLR was likewise filled in a short while ago. The replacing pedestrian crossing is red against pedestrians for much of the time that there is no traffic, so of course ends up getting ignored, then traffic is released round the corner from The Tower and there is significant conflict. Whoever thought this one was "safer" needs to go back to college. Notably both this one, and York Road at Waterloo, are borough schemes crossing TfL maintained London trunk roads. I wonder if there's some turf war between the two, either on political attitudes or over costs.