There are two different issues here.
Firstly the regulator is determined to control NATS costs. It has agreed an investment plan with NATS and allowed a certain amount of profit to fund that investment but if, in the regulators view, NATS has failed to control costs and instead of investing that money has used it to fund operating costs then in all probability it will take action to stop that.
Second the regulator has little choice but to respect Parliament's wishes and allow pass through of pension costs for those staff covered by the Trust of Promise and probably also has to allow pass through for any staff in post before it indicated that something had to change. However it is not obliged to allow NATS to continue to offer the same pension provision in the future. There is nothing in the Transport Act that requires the regulator to consider the view of NATS staff in it's decisions. The size of the potential costs to customers is such that the regulator may feel that it isn't meeting its obligations under the Transport Act if it doesn't do something. Certainly other regulators have already acted to curtail pension costs and it would be surprising if the CAA hadn't noticed that.