Of course she was real. She had a mother, history and upbringing. Now as to whether the post-death Thrace ( "the second coming" ) was the "spirit/angel" of Thrace or an altogether different entity separate from Thrace ( like physical Gaius and the "spiritual/angelic/head" Gaius you see at the end of the series ) that's up for debate.
Her destiny ( teased throughout the series ) was to sacrifice herself to lead humanity to salvation ( earth ). It's similar to Christ in a way - self-sacrifice and the second coming to lead the faithful to the kingdom of god.
I've watched through BSG I think 3 times over the years, and I've come to the conclusion that I don't think she was strictly human, in the normal sense.
I think from day one of her existence, she was a kind of power on the same level as Baltar and Six's angelic alter egos. Watching it the first time when it originally aired, I had thought she was one of the Five (even though part of me thought that was too obvious, and a cop out)... and then the fifth member was revealed and it wasn't her.
Clearly the writers had given her a role beyond merely human or Cylon, something part of the grand scheme of God that Messenger/Head Baltar and Six were part of.
