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As you said, cloacal extrophy is a pretty horrible birth defect. A quick search on google reveals that it has to do with severe defects of the urinary systme and abdominal tracts. Some children may be born without a anus and internally the colon and bladder may join up. http://www.duj.com/cloacal.html
It apppears that as recently as 15 years ago, many of these children died shortly after birth due to their inability to urinate and eliminate waste properly. However, surgery to create a functional urethra and colon has enabled them to survive.
Given this, I am not sure how you can be so dismissive of the surgery that was performed on these children or imply that surgery was done merely to assign gender. There are obviously some pretty serious functional considerations driving the need for surgery in these children.