Diesels mostly or completely under wires is an underuse of infrastructure, probably yes.
However everyone assumes that diesel engines are dirtier and less efficient, but it isn't necessarily true. A coal fired power station (around 40% of UK generation) is around 30-40% thermally efficient, a gas fired power station perhaps 50% efficient (another 35% of UK power generation)
An MTU 16V4000 diesel engine is around 40% thermally efficient.
So overall, the energy and carbon efficiency picture is not as it may seem. Compare re-engineering all the HSTs to building a new fleet of electric trains and electrifying swathes of the network and the lifecycle carbon footprint may be much worse because you have to build new trains and use lots of energy to enable them.
Electric cleaner at point of use, yes. Cleaner/more efficient overall? Maybe not.
That said, electric trains can run off any electricity, they don't care how it was generated. Increase of nuclear, biomass, geothermal energy etc will cause no issues, electric is future proof. Bio-derived carbon-neutral synthetic diesel is on the way but is probably harder to ensure these are backwardly compatible with existing diesel engines.
Nevertheless, the transition from fossil to renewable will not happen for perhaps 30 years, we'll still depend on coal and gas for our power, we'll still drive cars (and trains) fuelled mostly by petroleum.
I will get shot down for this (!) but there isn't really the business case yet for investing in vast electricification projects in this country on existing lines (e.g. GWML) particularly in our parlous state. Of course, any new projects should and will be electric and in-fill electrification for operational reasons is the right thing to do.