suggest a different theory for ITV encrypting these regional feeds: they want to move ITV HD onto Astra 2D from the wide beam it is on at the moment.
Why would they want to do this? Because a lot of non-freesat set top box makers have updated their firmware and ITV HD can now be received all over Europe. That will limit what they can broadcast on it - they already have to use 2D to broadcast their low-def channels, the studios that demand this will be even more up-in-arms if their programmes can be received in HD without similar constraints.
So what I think ITV are doing is to prepare for a bit of shuffling of the channels around the transponders, moving the encrypted ones onto a wide beam, to make space for the bandwidth needed by ITV HD on Astra 2D. From the number of affected channels, the total relinquished bandwidth does seem to be "about right" for the space that ITV HD needs.
Of note is that they have only scrambled channels which are sub-regions, i.e. Tyne Tees South is now encrypted, Tyne Tees North is not, the same for Yorkshire, Anglia and Meridian. This I suspect is to limit the impact on Freesat and FTA viewers (Sky digibox users with a valid FTV card will be unaffected anyway as they will still receive the encrypted channels) since ultimately the only thing they will lose is the tiny sub-regional news bulletins within the ITV1 regions news magazines. Any loss of advertising directed at the sub-regional level will be minimal since most satellite viewers of ITV1 will be using Sky and they won't be affected. Those who can no longer receive Tyne Tees South (or which ever sub-region they have lost) still have their other sub-region (Tyne Tees North etc) available, still unencrypted, and this channel is the same as the one they have lost for 99% of the time so they probably won't notice anything.
So I see this as being a "least worst" option for ITV to try and get their HD channel over to Astra 2D with as minimal an impact on viewers and revenue as possible.