Everything National Express did during their tenure of the East Anglia franchise was about reducing cost. (e.g. reducing the Shenfield service to 4 cars outside the peaks and at weekends). Obviously it had to work operationally too, but the financial saving of moving out of Hornsey was too big to ignore. The poor old 306 didn’t stand a chance against the mighty NX financial machine.
I'm as saddened about it as you, but when you've got an operational railway to run you can't afford to have half a covered road taken up by a failed non-operational unit like the Cl306, especially when the size of your allocation is about to expand dramatically. Notwithstanding any issues about the non-fitment of safety equipment (I'm still unsure if it had TPWS) it needed a new HT lead to connect the pan to the transformer which was going to be a bespoke item due to it being longer than on existing units, and therefore not the sort of thing hiding at the back of a shelf in the parts store, and was going to cost an eye-watering amount to have made. The chances that it could ever have been made to run again even at that point looked slim.
The penny-pinching didn't start until a fair bit later in the franchise, by which time the Cl306 had already gone. We had the same issues with the Stansted Express being split and then reformed during the day to save mileage on the units. Gone too was the notion of a specific fleet of Cl317s to operate that service because they were accumulating mileage far quicker than their classmates with the consequent effect on the scheduling of exams.
As for the savings achieved by taking the units out of Hornsey, I've no doubt that it make financial and operational sense. However, as I said above, I'm not sure that the decision came from within the company but rather was imposed on them by the DfT. Prior to WAGN ceasing to exist and the GN side being grouped with Thameslink to form First Capital Connect, the WA side at least remained under the NX "London Lines" grouping together with WAGN, c2c and Silverlink. However, once the split had occurred there would have been an imperative to split the operational and financial dealings of each company wherever possible so that any issues suffered by one did not impact on the operation of the other.
Mind you, Hornsey did have the last laugh by "stiffing" Ilford over the Cl317 spares which should have come over with the fleet but didn't. There were even rumours that items such as traction motor snow screens just ended up in a skip because Hornsey decided that they no longer had any use for them. You can imagine the impact this had on the reliability of the fleet.