You're right. Although I am much more likely to trust someone who has had significant experience with both (especially if they have also managed to become a doctor or something similar).
I don't have much information, but based on the article, I believe this doctor is biased by the fact that he has focused only on the very rare cases of individuals which develop an obsession with the drug and continue to use it even after it's primarily sought-after effects have stopped working. If you use MDMA every day for a prolonged time, then you are definitely going to get brain damage.
The reason this generally isn't a problem with MDMA is that, long before this happens, you will use up all your serotonin (temporary) and the drug essentially stops working, even with increased dosage. This usually means that people stop taking it before any major damage is done. Contrast this with opiates, where you can keep upping the dose and keep the high going indefinitely over a prolong time (until you overdose).
I dismiss the doctors statements not just because he hasn't done these drugs himself, all I need to do is look at the number of heroin addicts in rehab vs the number of chronic MDMA users.