L.R.
K., I'm sorry about this! It's tough to know what to do because few kids seem to experience it. My daughter, now 10, is missing one permanent tooth, which we know from the X-rays; she has a baby tooth in that space now and the ortho and dentist (who work well together for us) say, leave the baby tooth alone and we'll deal with the gap much later -- for girls, the ortho says, they don't do implants until quite late, even later teen years.
What does your son's dentist say about the orthodontist's insistence on pulling teeth? I would bet the dentist will be against it. Does your orthodontist share information, x-rays and diagnoses with your dentist? Ours does and it's a big help.
I'd definitely get a second or third opinion from other orthodontists. Around here, orthos. give free consultations for new patients; you can check with a couple and tell them you would like a consultation on this particular issue and it might be a free visit....In the end, the doctors are the experts, but I do wonder at this eagerness to yank so many teeth at once in a kid this age. We saw one ortho who wanted to start yanking my daughter's teeth because some were going to come in funny, but ended up going with the ortho who said no, we can fix that without pulling teeth....