I don't see why this is a difficult topic, or why they're trying to push transgender issues on top of intersex issues.
Is there a problem with the genitalia that needs to be addressed in order to function without infection/disease/problems? If so, fix it. If not, leave it the fuck alone until the person can decide for themselves what they want done about it.
Same goes for any sort of medical stuff for children and infants. Is it critical that it needs to be done now? If so, do what you need to do to ensure the person can live. If not, wait until they can decide for themselves. Is that so hard?
If it's an issue like the individual mentioned in the article, just make a note of it in the medical records, in case some sex specific thing is to come up (do men/women/intersex get different treatments anyway?)