Perhaps I am a little naive, but if I boarded a "fast" train at Waterloo, I would be rather disappointed if it began slowing down minutes after departing to stop at a station which already has plenty of services calling there.
Surely the solution is for a passenger waiting at Clapham Junction wanting a fast train to take the first available train to the first stop where the fast train calls. Clpaham Junction is a little too close to Central London to be a stop for fast trains.
I emphasize that this is my personal opinion with my own expectation of what a fast service should be - a limited stop service.
The first stop other than Clapham Junction for fast services is Woking. The slow service from Clapham Junction-Woking is only two trains an hour, taking about 40 minutes. A fast service from Clapham Junction-Woking takes about 20 minutes. Enough people use Clapham Junction to justify stopping fast trains IMO. Where fast trains stop should be directed by station usage IMO, not how far they are from other stations.