I've had that happen to me, most of the staff in Boots will refuse to sell me anything more exciting than a paracetamol if i tell them i have diabetes incase it makes my blood sugars go wacky (as if they're not already...). Flunconazole in the capsule is apparently one of those things, although is says absolutely nothing about caution in diabetes in my reference book (BNF). I'm had similar problems with buying ibuprofen and cold capsules with decongestants. I think it's mostly a duty of care thing. If a doctor prescribes it it's his fault if you have side effects or in the unlikely event of hypoglycemia. If the pharmacist sells it to you over the counter it's his problem.
I've used the cream, Clotrimazole and that's worked for me. Do buy the own or generic brand though, the price mark up on Canestan is quite high. I'm fairly sure you can't buy the Fluconazole capsule alone over the counter.
I hate having thrush, I usually get it after or while taking antibiotics and in general, I preferred whatever it was I was taking the antibiotics to get rid of....chest infection, urinary tract infection, tonsillitis...It took one week to get over those and another week and a half to clear the thrush. I can't blame you at all for feeling miserable about it, it's vile.