I'm sorry, some of you crack me up. An 18 y.o. was attacked in a restroom. So what does that mean? Moms should take their 18 y.o. sons into the ladies' restroom, and dads should take their 18 y.o. daughters into the mens' restroom? Someone was attacked by a guy with a knife in a restroom? Maybe you should just squat in public where no one can hide.
Hate to break it to you, but you cannot eliminate all risk. I feel sorry for the grown boys being dragged into the ladies' room by their moms due to irrational fear. Your children stand a much higher risk being injured or killed traveling to and from WDW than they do being attacked in a restroom while there.

I love the pp that mentioned a boy having his throat cut at a urinal, like that happens every day. Just a few months ago there was a crazy guy who pulled out a knife at a Dave and Busters and stabbed a young boy playing a video game. His parents were in the same room, near him. There are the occasional wackos and if you come across one who wants to harm you there not much that's going to stop them. Fortunately they are few and far between.
As far as the OP's situation goes, considering she is still bringing him in the stall I'm assuming his delays are severe enough that he actually needs assistance in the bathroom. If that is the case I would try for the companion restrooms but would use the ladies room if they were busy or far away. If you have a child who is unable to actually use the restroom alone that is far different from a parent who is just afraid of their child being alone. In the ladies room you will probably get some stares if your son does not appear disabled.