I am sure cost is the part the PCTs care about. But far worse for individual doctors (whether GPs or consultants) is that they endanger their own careers, reputations, etc.
This occurs because of the controversial status of prescription desiccated thyroid as an unlicensed medicine. Thus the entire responsibility is on the shoulders of the prescribing doctor.
The fact that the establishment endocrinologists repeatedly claim that there is no place whatsoever for desiccated thyroid - so anyone who does prescribe it must be a rebel, a maverick, irresponsible, dangerous and so is to be suppressed.
Ironically, it is much cheaper for you to buy it on a private prescription (e.g. directly from Erfa in Canada, and ignoring anything paid to the GP for prescribing it) than for the NHS to supply it. When dispensed in this country it is handled by a company such as Idis with consequent high costs and margins.
Note 1: I try always to use the term desiccated thyroid rather than the brand name Armour (or Nature-Throid, Erfa, Thyroid-S or whatever else) - adding 'prescription' and 'porcine' if needed to distinguish it from some of the other 'glandular' or non-prescription products.
Note 2: I am no blind fan of desiccated thyroid. Though I have seen it considerably improve someone near to me, it is not the 100% answer for everyone.
Note 3: There certainly are circumstances in which private prescriptions can be issued by NHS GPs - for example, I think some vaccines and 'holiday medicines' are provided in this way.