Your gp is talking nonsense.
There are limitations on certain drugs being dispensed via electronic prescription. It is not currently possible to use EPS to dispense schedule 2 and 3 controlled drugs -
https://www.chemistanddruggist.co.uk/news/no-controlled-drugs-eps-until-2018
But, and this is the big important but, needles are not in any way, shape or form a controlled drug. You can buy them without a prescription on Amazon. Needle are not a schedule 2 and 3 controlled drug, the only drugs currently excluded from EPS.
If you have confirmation from your CCG that this should not be an issue, get that confirmation in writing from the CCG.
Write to your GP practice to get them to put in writing why they aren't dispensing needles via EPS.
Then you can put in a complaint to show that they are contravening the expectations of the CCG, complain to the practice and the CCG because I imagine the CCG will give them a kick to get them to resolve it.
In the meantime, do you actually have to pick up the paper prescription? I don't use EPS because I'm easily defeated by technology. All I do is take my repeat into boots with what I need ticked off. Boots take the prescription to the GP surgery, get it signed and collect it to dispense the meds and the text me when everything's ready to collect. Can you have a chat to the chemist to see if the offer something like that to at least cut down some of the steps your having to go through while you GP practice gets over their weird needle phobia?