Indeed, but they didn't know that was going to happen when they authorised the GWML.
Are you sure you're not recycling the political justification given at the time? Surely "they" knew that the HSTs on the MML were going to have to be replaced if the GWML ones were.
The HSTs have always been far more suitable for the long distance GWML, rather than the regular start-stop service pattern on the MML, so the MML's need for electric rolling stock with superior electrification was well known at the time.
The case for the MML electrification had been known for so long, in fact, that far more preparatory work had been done for it. I recall genuine surprise (and some astonishment) that the GWML had overtaken it in the priority list.
Given the lack of electrification experience and skills that Network Rail had in recent times, the huge ask of electrifying the whole GWML on which precious little preparatory work had been done was a very big risk....so not surprising when things started to get so out of hand, particularly in terms of not knowing where signal cabling was and cost over-runs.
I still maintain it was the wrong decision, and people should have known it was a bad decision at the time. The rolling stock issues could have been solved in different ways, as the bi-mode technology is now demonstrating.