Whatever the merits (or otherwise) of the requirement, it must be taken in the context of PPL training & testing throughout Europe. In all other EU member states (as far as I am aware) the PPL examinations are run by the national authority and, in this context, the requirement for all exams to be passed in 6 sittings is of little consequence.
The Aircrew Regulation was always going to be a compromise, with some States' opinions winning in some areas and nobody entirely satisfied. In the case of the PPL theoretical knowledge examinations, it was clearly not the UK's position that prevailed, not least because the CAA was unique in the way that PPL examinations were handled. In fact, it was pretty unique in the way that it generally ignored PPL training organisations unless or until they drew themselves to its attention (I'm not sure there's another authority in Europe that would have had to admit that it had no idea how many RTFs there were in operation!). The fact is that the resulting text satisfied the majority of member states and is now EU law - the UK will just have to live with that.
Given the requirements for PPL training organisations to become ATOs, it will be quite simple for the CAA to require that the management system documentation includes a process for managing theoretical knowledge examinations. The management process having been approved by the competent authority, continued compliance will then be a subject for audit and a requirement of continued approval. After all, there is already a requirement for the ATO to provide 100 hours of theoretical knowledge instruction and, before recommending him/her for the examination, to confirm that all elements of the training course have been completed to a satisfactory standard.
My understanding is that the 9 exams are currently in course of production and are due to be introduced in March/April, despite not being in compliance with the Regulation. It is also rumoured that plans are well advanced to do away with the current system of designated custodians and to centralise the PPL examination process, possibly on-line, which will better enable the monitoring of attempts and sittings, not to mention the security of the examination papers.