I work at a dental college, so I know 'just enough to be dangerous'..........take this for what it's worth.........
Braces CAN be medically necessary, but it all depends on your son's situation. Your son's teeth may not be straight, but you have no idea whether he chews okay. Have you gone to any of your son's appts. and talked to the orthodontist personally? One valid concern is occlusion...how the teeth meet together. You don't say how old your son is, but if he's still in his teens, his teeth will still be moving. And if his wisdom teeth come in sideways (as they often can do), it will wreak havoc on his alignment and occlusion. And a mis-aligned occlusion can certainly cause problems down the road....TMJ is just one possibility and that is VERY difficult to get treated. That one I know personally because I work directly with the pathologists who see TMJ pts.
If she is asking for ONLY $1000, you're getting off dirt cheap. SS was able to go through the orthodontic program here and I was also able to get him the 'employee's family' rate, but the total cost was still between $2000-3000. Around here, going to a private orthodontist it would cost up to $10,000 for braces. Here we can set up a payment plan with the college and pay a set fee per month towards the contract until it's fulfilled, so between DH and BM, they traded off paying every other month.
I recommend going to your son's next orthodontic appt. and talk to the DDS personally, so that you have all the facts. If your BM won't allow you to do this for whatever reason, demand to see a copy of the DDS's notes outlining the reasons for the need for orthodontics before you'll agree to anything. You can also shop around..........if you have a dental college somewhere near you, I'd certainly take advantage of that. Student fees here can be anywhere from 1/3 to 1/2 less than a private DDS and they do EXCELLENT, thorough work..........I can vouch for that, at least from this college!