odd... did he explain why he wouldn't prescribe the smaller dose? and did you ask if you could get it in liquid form?
i don't know much about the gp system over there, but here in the UK, most people who want LDN end up having to see a private gp, as the NHS ones and NHS consultants generally do not want to give prescriptions for it.
i get mine this way - i saw a private gp as a one-off consultancy, paid his fee for that meeting, and he now just sends repeat prescriptions to the pharmacy for me, and i pay the pharmacy for each bottle... is there any such system where you are?