Merging issue

So, I recently rejoined the WoW community here as I have not been on here in a year. I returned to find I will need to merge my character to Icecrown. Upon doing so I was forced to change her name, and lo and be hold I merged of course but on the wrong faction!! I was on alliance previously and I am baffled how my character after merging ended up on the faction that I did not choose. Anyway if someone who is able could please get back to me, and talk with me about this that would be great! I am not sure if anyone else experienced this, but I'd like to be able to fix this issue.