[quote=@Bright_Ops]
...What exactly would you think the Jedi Temple's stance on trans-sexuality would be? They are a highly conservative religious order that disproves things like strong emotion, personal attachment and emotional relationships of any kind. They also discourage jedi marrying each other because they fear the creation of powerful force dynasties. 

Personally I feel that its one of those grey areas that the Jedi Council refuses to call one way or the other because it seems more like a decision that every individual jedi needs to make for themselves on how they feel about it.  
[/quote]

I can't imagine there's an official stance on it, but I don't think they would care overly much. Considering all the weird shit that's in the known galaxy, and the fact they have members from dozens of different species and cultures, I can't imagine transgendered Jedi would be even something that would come up as taboo or weird.