Hi there. Completely stumbled upon this site and read this thread, and thought i'd post a quick reply.
As a nurse in a veterinary practice I can understand your concerns but not protecting you pets against fleas and worms is not advisable! They should be treated every other month with frontline, or every month with advocate. The treatments sold in a clinic are the best around, and if others worked then they would sell them(it would save them money aswell!) Homeopathic remedies are genuinley about as usefull as spraying your dog with water! Some supermarket products do work. My dog is allergic to frontline and uses a flea treatment from wilko's that work fine for him, however all dogs are different!
I would definately call and speak to a nurse/vet at your clinic and explain your situation to them. If you still feel you are being fobbed off then ring around vets for second opinion.
Also please don't consider not vaccinating your dog. I understand your concerns with the chemicals in the treatments but vets only use these chemicals if completely necessary. I'm sure they would all rather be using herbal remedies as they are handling these chemicals all day, everday, but at the moment that just isn't a possibility.
Lastly the vet only has your pets best interests at heart! Unless your vet is the owner/partner of the practice they are not pocketing ANY more money than they would if you don't take the treatments!
I really don't want to sound pushy, but when you see pets coming into a clinic with roundworm it puts it all into perspective! Maybe browse the frontline and advocate websites to see what chemicals are involved in the remedies, or email them with your concerns.
I hope it all works out well for you!