From her letter:
“I wish to see the impacts on the taxpayer and on overall performance for passengers – such as potential congestion on the network – given primacy when considering open access applications.”
While hopefully it was never her intention, there's a way to read that as meaning she dislikes the fact 3.8m passengers out of 23.4m on the ECML (stat from the OP article) are getting cheap fares compared to what a state operator would charge. So she would rather the rules were tweaked to say these journeys aren't utilising spare capacity but are preventing the state operator from running more trains using these slots. Which they probably won't do if Sunderland is any guide.
Without knowing whether GBR intends to use branding in conjunction with low fares on spare paths it has available to use but aren't worth running as part of the main offering, I don't know how you can say whether passengers will be better off without OA potentially attracting custom the railway didn't have before (perhaps because the need to change trains or book far in advance negates any slim advantage the train has over the car).
If the vast majority of those 3.8m journeys are thought to be individuals getting a free ride off the backs of the 23.4m, not innovation driven extra demand (wouldn't that be an incredible boost for the underlying theory of railway privatisation if it was), then surely the far bigger waste of taxpayer funds that OA represents is the need to have a system of track charges, delay attribution, and a statutory body acting as an impartial arbiter of meritorious applications.
But if Labour aren't going to nationalise privately owned feight TOCs, Heathrow Express and Eurostar, and all charter operators too, then what are you saving really? It's her role to explain that, not the ORR. It's her job to know why the railway does things the way it does, and tell them how to do it differently if it conflicts with the government's priorities.