Ek = 1/2 mv^2, yes. However, that assumes that instead of doing hundreds of miles cruising at 125, it's instead doing the same at 75, which simply isn't the case. The trains are stopping and then accelerating back up to line speed much more frequently, which would strike me as putting more stress on the trains. ISTR this may show in the traction motors failing for Scotrail more, even if the MTU units fare alright with this sort of work.
For example if we look at the
1H51 today, it's travelling 180 miles from Queen Street to Inverness, but it's stopping on average once every 18 miles even if we assume the single track sections don't cause it to need to stop anywhere outside of scheduled station stops.
I think it's fair to say that is much more frequent than anything they'd have been diagrammed to do on the ECML/GWML.