Kathleen and I have been spending a fair shake of our time looking through the interwebz at the whole Judge Rotenberg Center issue. There are hundreds of pages of materials to go through, and heck there's 115 pages just from Israel's response to the UN outcry and Nightline report.
For Israel's take on the history of the center, you can read his interesting article at his site. Israel writes:

"In this respect, JRC is like a medical hospital. The goal of most medical hospitals is to return the individual to good health and to a normal living situation outside the hospital; however, in order to reach that goal it may be necessary to do some highly “abnormal” procedures within the operating rooms and in the emergency and intensive care wards of the hospital." 
Does the JRC do that, though? How many clients leave, all better? The responsible thing to do would be to compare the JRC to other residential facilities, what restraints, aversives, and positive reinforcers they use.
The problem is that Israel's client base appears to have shifted (page  of the report) over the years so that it now consists more of emotionally and behaviorally disturbed than autistic or ID clients. And, so far, there doesn't appear to be enough transparency in how many graduate and leave, and how many new clients they get.
Israel seems to go on and on about not warehousing, but if 5 of his 6 "success" cases are decades later still at the JRC, they are not success cases.
None of his aversives in his power points (which don't appear to have been shelved, from what I can tell) can be used on clients in Texas facilities for the disabled. They can't be used on inmates in a jail. If he still places clients in restraints (and he does) and then while in the restraint (and he does) has them shocked, this is, at best, problematic. The pinches, presses, spankings with spatula would all be considered abuse if done by a staff member. Restraints, including chemical restraints, are being restricted as well. Times are changing (that's for damn true, as Thelma would write).

And Israel thinks that it's perfectly legitimate to do a trial run on a kid so he knows what the result will be if he acts up:

"Preventive use. In the case of a few of our students, we successfully employed a preventive treatment, called behavioral rehearsal lessons. In this procedure, the student practices the initial phases of a problematic behavior and receives a GED application when he/she does so."

If you've got a backpack on at all times, and you can be shocked for any behavior deemed an antecedent behavior (and it's direct care staff doing the shocking), you've got a powerful incentive to behave. The question becomes is this an ethically acceptable way to maintain compliance, through fear? My moral perspective is that it is not. If you clamp down tightly and make every single privilege (involving food choices as well) contingent on desired behavior, you're also ruling through fear. It doesn't even appear to use the science available regarding reinforcement schedules or on fostering internal motivation. So, do these students, if they leave, know how to behave without the heavy hand of Israel and his staff?
They send the remotes to shock and the backpacks home with the parents. How is that okay? Parents in control of the clicker and able to give their child repeated 2 second shocks. Is anyone monitoring that? The court may approve the shocking, but are they reviewing every shock administered? Is anyone?  And apparently, despite the safeguards of giving the client a lawyer and psychologist, the court rarely rules against the shocks, because if the individuals were competent, of course they'd choose to be shocked. Not by a long shot, is what I'm thinking.
We know that abuse of the disabled occurs in residential facilities and a better job of cracking down on those abuses needs to occur. Cameras can help. But the JRC has cameras and the young man was still put into a restraint and shocked at least 77 times, all while the cameras rolled and staff milled around. Of course, the center then destroyed those tapes despite being ordered to preserve them.
The JRC represents one institution. Maybe there are successes there.  Maybe the center isn't any worse than others that house the emotionally and behaviorally disturbed (and a smaller proportion of autistic clients). But maybe the swank digs and opulence simply better hide a rotten core. I don't know. I honestly don't.

 But I know it serves as a beacon to society to really consider the ethics involved in caring for the most severely disturbed individuals in our society, and extending it out, the most severely disabled. It's a human rights issue. We should each have the right to not live in fear. I'm not certain that any of those there really have that. It's pretty powerful to have more people with a backpack on than not and to know that if you don't fly straight you can have a backpack, too. And that someone with three weeks worth of training can decide whether and when and how often to shock you.
What is the Justice Department doing on this? How much inspection is occurring?  Parents insisting that the shocks have saved their children doesn't mean much. I've read far too many parents who write just as passionately that vaccines damaged their kids, that Soma or FC has recovered them. Anecdote in the place of evidence is meaningless white noise, you know, like Israel uses as an aversive.

 from here