I had Nicky microchipped as an adult, Rally as an older puppy and then my others are 8 weeks. Nicky flinched signifcantly when they put his in resulting in it being off to the side. Most of my pups done at 8 weeks also ended up with them slightly to one side or the other. Rally is the only one that is pretty much centered.
I do think that those of us with well behaved dogs take for granted how truly difficult it is to handle a dog that is not used to regular handling. I don't just mean risk of getting bit either, I mean just a young adolescent dog with no self control. Working in the shelter, I see lots of dogs like this, any physical contact puts them over threshold, they wiggle and squirm and if you think a puppy is bad, imagine that same reaction in an 85 pound adult.
That doesn't excuse rude behavior on the part of the vet or their technician but it is the reason many do microchipping during spay/neuter procedures. I would probably start looking for another vet also if their attitude is as bad as it sounds. You need to have a vet that will listen to you and that you can trust.