In the version I've heard, Churchill had planned what was quite a circuitous route from Waterloo (Paddington having been the official choice), but told the military officer sent to seek his approval for the plans that in the event de Gaulle predeceased him, they could depart from wherever they liked.
Edit - sadly perhaps not true. Brief research on the Internet produced this:
At first sight, railway geography would seem to support the myth. To get from London to Bladon, Waterloo would not be your first choice of station. The obvious departure station would be Paddington, from which a train can get to central Oxfordshire very directly. However, if the organisers definitely wanted to include a journey down the Thames, the problem is that Paddington is a long way from the river: it would be a case of a road procession from St Pauls to Tower Hill, a barge from there to the West End followed by a second road procession through Mayfair and Bayswater. Waterloo is not only almost on the riverbank, but there is a fairly direct rail route from there to Reading, where the train can join the main line from Paddington and on to Oxfordshire. Moreover, for obvious reasons the train was hauled by the locomotive “Winston Churchill”. Although the railways were nationalised in 1947, in England and Wales the former railway companies had survived as largely-autonomous “Regions” within British Railways. “Winston Churchill” was built by the Southern Railway, and in 1965 (although only a few months from withdrawal) was based at Salisbury, on the Southern Region’s lines out of Waterloo. It is probably safe to say that at that time there were no loco crew at all on British Rail who were qualified both to drive “Winston Churchill” and to drive trains from Paddington to Reading; on the other hand almost all Waterloo-Reading line steam crews would have been able to handle the engine. It is also likely that special work would have been needed to make sure that a Southern Region engine would even have been able to run on the Paddington-Reading line safely. In other words, using Waterloo solved two issues: how to get the procession from boat to train easily, and also how to ensure the right engine could be used on the train with minimal special effort. I hope the above is helpful to you. On balance, I think it is highly unlikely that the use of Waterloo was purely to annoy De Gaulle – although I can imagine that when it became apparent that Waterloo would be the most straightforward terminus to use, it would have raised a few wry smiles on the planning committee!’
(From 'Beachcombing's Bizarre History' here).