The wider system I'm to which I'm referring is the rest of Thameslink. It is a system which needs to shift as many people as it can, therefore it makes sense to make decisions which inconvenience some people BUT result in more trains being able to operate on the busiest sections.
The problem is flat junctions. Just south of Blackfriars, the trains via London Bridge and those via Herne Hill need to cross each others' paths. If there was a grade-separated junction this would not be an issue. Having Wimbledon and Brighton services interlacing over a flat junction will reduce the number of trains per hour you can run on the line. It is a bottleneck. Off-peak there should be plenty of redundancy to run through services, but during the peaks you will be limited because of junctions like these.
If you were to, say, terminate Wimbledon trains at Blackfriars and keep trains via London Bridge running through, you remove this junction problem altogether and overall the number of trains can be increased, because the two sets of services never have to interfere with each other.
The price to pay is cutting back a service and making people change trains, which in central London for commuting journeys is not a real problem, more of a mild inconvenience. The reason I used the long-distance service to compare was because, for long distance travel, passengers tend to have a lot of luggage which is bulky and time consuming to move. Commuters with their backpacks and briefcases won't have the same difficulty in changing trains.
Of course, there are bottlenecks elsewhere, but from an operational point of view it is madness to have services interfering with each other on the busiest sections of your line. If you look at the approach to any London terminal (and a bit further up the line), they normally have some form of grade separation to allow more trains to enter and exit the station (or diverge onto suburban routes). Installing a new junction like this at Blackfriars would be hugely disruptive and expensive. As I said before, a cheaper and workable alternative has been found, but apparently it's too much to ask for passengers from the Wimbledon loop to walk ALL the way across the platform at Blackfriars to catch a connecting train.