I am going to try to go through this bit by bit. I am trying to be respectful of the OP, but there are lots of things that just don't compute right in my brain on this topic.
First, I would think that not labeling a 6 year old as being transgendered and/or having a gender identity issue would be wise. Kids in that age group are still working on establishing for themselves what gender roles are and where they fall in the whole grand scheme of things.
I am very curious as to why you would take your son to BBB in the first place. Again, I am not trying to be ugly about this, I am trying to understand your motivation. If your son is "girly" are you trying to promote that in him? I have met my fair share of long haired "girly" little boys and none of them ever expressed an interest in
becoming a Princess, let alone going for a Princess Makeover in such a public place? Yes, many of them wanted to play dress up and take on "girly" roles, but that was all pretend, and they knew it. Most children in that age range don't even know what BBB is unless someone tells them that it exists. Did your son ask for this?
Now, with that said, I can see where the staff would have been very taken aback by your request. I fail to understand how you could have been "floored" by their response. Your request for services for your son are not even on the radar of normal for the majority of the people walking on this planet. Some people might even feel that doing a Princess Makeover on a boy was not nurturing at all, some might consider it to be child abuse.
I am sorry that your son needs medication to get through life at such a young age. That stinks. I would hope that all parents do seek to do things in the best interest of their children. Fighting the good fight is part of any good parent's job. I am glad that your vacation ended up being a good one.
Since you have made all of this so public already, would you mind explaining exactly what the psychiatrist told you? I am sorry for being so ignorant, but I just have never heard of someone so young being diagnosed as having gender identity issues. I am also curious to know if the psychiatrist had anything to say about you taking your son to BBB.
Then, basically, you wrote that your son is still your son, and as such, is just "girly". Can you share how your son is "girly"? I am just not understanding from what you have written so far as to how he is having gender issues.
Learning who he is largely comes from the information that the parents and society provide to him at this age. I have to wonder if a Princess Makeover at BBB and having strangers calling him "Princess" is the right message to be sending to him, if he is going to remain a boy? I can't imagine the questions that must have gone through your mind in planning all of this. Can you help me to understand? I realize that you don't have to, but I am just confused.

To me, it seems that either he identifies as a girl and should be treated as such (in ALL areas - home, school, WDW, etc. including using the restroom of the gender he identifies with) OR he is still mostly a boy and should not ask to be addressed as "Princess". It just seems like there is too much gray area here. I swear, I am not trying to be mean in saying any of this, really. It just seems that waffling on which gender to treat him as 100% of the time would not be sending a clear and consistant message.
I will keep you all in my prayers. From what you have posted, it sounds like there are lots of issues for your family to tackle. Things will work out over time, just keep moving forward.