They have, and you are dead right - however that is a political decision that I don't see being reversed any time soon, which is unfortunate as I would much rather see that outcome as well.
It is, but at some stage high fares become a political issue as well (although passengers don't have the same ability blockade the fuel depots that the road hauliers do)
It is a policy that has been operated at times over the entire history of the railway, because the cost of meeting demand has exceeded the income that meeting that demand can generate. It is noticeable that this has especially happened in railway history when "public service" requirements have limited fares.
The public service provided by the railway network is the ability to travel. Your, mine or anyone else's ability to make that journey is a private benefit - as is the ability to do so at the price you would choose to pay.
As for what Westminster and Whitehall may do with it, can I remind you that a nationalised organisation is owned and controlled by the government - and that they have very broad discretion as to how they have those services managed. Subject to the verdict of voters, which will depend on many factors, they are entirely at liberty to make the railways entirely commercial - or to make them entirely free to use.
I've seen this argument about limited capacity, but I've yet to see any evidence that demand on the ECML is so routinely overcrowded that:
a) it is being driven be large numbers of off-peak fare holders.
b) it can't be managed in the traditional way by having more or fewer advance purchase fares.
This is why talk of capacity is a red herring. It's about getting more revenue.