These two excerpts are interesting (my emphasis):
"The mental twist may be prompted by faulty early training, or it may be because of an inherent mental weakness or a protest against conforming to the practices of the herd, or, and this is most probable, there may be glandular pathology or simple grandular imbalance."
Apparently even then, knowing virtually nothing of all we know today, they saw physiological causes as "most probable". Obviously, the specific explanation above has proved incorrect, but yet, even in 1947, doctors did not jump to the conclusions that conservatives still often jump to today.
The second is from the quoted letter from a sexology journal further down in the article:
"It is apparently true that Nature has created female minds and bodies and endowed them with male sexual organs. Likewise she has apparently created male minds and bodies and endowed them with female sexual organs."
This is rather radical, given the time it was written. While their recommendation was not what we'd like to see, we have to remember that at the time, SRS was almost guaranteed to kill the patient.
Of course the language used in much of the article is offensive to us, but most medical language from that era would be offensive today. Open any medical dictionary from that era and there's (by today's standard) derogatory language and slur words everywhere - that is, they probably weren't at the time, but medical terminology has a bad tendency of having to be replaced once every few decades since they're adopted by the common population as slurs.
