Basically, what had happened was the demand modelling they used in the 1980s, which was really one of the first of its time said the passenger numbers would reach 25-30 million by the end of the 1990s. Hence the enormously long trains that were ordered for Eurostar. In reality, the passenger numbers were less than half of that, maybe just a quarter (without looking at my books). Anyway, British Rail by the end of the 1980s realised that Waterloo couldn't cope with 30 million Eurostar passengers a year, so they looked at building a new terminal. White City, Stratford and Kings Cross were the contenders, with a large combined underground Thameslink/Eurostar station built at Kings Cross-Kings Cross Low Level. The project became a pet of BR, who even started the legal procedures to build the station.
The original route for HS1 was the run the line I think to Swanley or Sidcup, then run under Hither Green, Brockley, the Old Kent Road and the City in a tunnel up to Kings Cross. Waterloo was going to be kept, as I understand it, with a spur that would have branched off the mainline somewhere underneath Brockley and joined the Catford Loop at an area called Warwick Gardens in Peckham. This would have served Waterloo bound Eurostars and Network SouthEast's "Kent Express" Networkers-now known as South Eastern Javelin services. Although I have also seen that NSE trains would have terminated at City Thameslink.
Anyway, by the early/mid 1990s they realised they wouldn't need two termini, so Waterloo was going to be closed. Hence why the Eurostar runs round London to approach it in the wrong direction. It made perfect sense in the 80s when Waterloo was still going to be open.