Was the machine written off?
No, it was fixed up, and returned to the RAF VIP fleet.
to provide clearance over all of the obstacles (some may have been removed now)
Actually this is a strange one, the key obstacle clearance landing at London City on 28 is based on clearance over the East London River Crossing bridge - which hasn't been built yet.
Picture here The picture appears to be looking along the 28 approach at ground level.
The bridge will cross the river at the same point as the approach to 28 crosses the river. Its height is a squeeze between clearance above shipping in the river, and clearance under the flight path. There has been a great amount of shilly-shallying over the project over many years, still not certain it will ever be built.
how can one hit a bus for Christ sake
I'm sure not. But I can tell you, as one who has been on the upper deck of a London bus on the roads across both ends of the LCY approach as someone comes over the top, it sure does look (and sound) close, and some of the other less aviation-aware passengers do duck - no quite certain what good that might do them though !