I'm pretty sure the Theodora they have in the game won't be Justinian's wife, but this Theodora: http://en.wikipedia.org/wiki/Theodora_(11th_century)
I am 99% sure it is Theodora the Wife of Justinian I. As she was also in Civ III the Byzantine leader and Theodora you suggested had hardly any power and ruled only for a very short period (along with her sister Zoe).
she was co-empress with her sister Zoe for two months in 1042 and sole empress from 11 January 1055 to after 31 August 1056.
Hopefully I'm wrong. Though if they are representing Justinian's wife, it'd be strange not to have Justinian in the leader screen too. Theodora (Justinian's wife) was the power behind the throne, not the power on it.
Yeah, kinda like this:
Additional info:
http://www.civ3.com/conq_prof_byzantines.cfm
Empress Theodora (Wife of Justinian I)
http://en.wikipedia.org/wiki/Theodora_(wife_of_Justinian_I))
Theodora is perhaps the most influential and powerful woman in the Roman Empire's history.
Theodora is considered a great female figure of the Byzantine Empire, and a pioneer of feminism, because of the laws she passed, increasing the rights of women. As a result of Theodora's efforts, the status of women in the Byzantine Empire was elevated far above that of women in the Middle East and the rest of Europe.
http://www.infoplease.com/ce6/people/A0848391.html
Theodora d. 548, Byzantine empress. Information about her early career comes from the often-questionable source, the Secret History of Procopius. It appears that she was the daughter of an animal trainer in the circus, and that she was an actress and prostitute before her marriage (523) to Justinian I, who, on his accession in 527, made her joint ruler of the empire. A stronger person than her husband, she helped save the throne through her energetic action in the Nika riot (532) In her youth Theodora came under the influence of the Monophysite sect; Justinian's efforts to reconcile the Monophysites to orthodoxy were probably inspired by her. She is represented in the mosaics of the church of San Vitale, in Ravenna.
Would be cool if she looked something like this in CiV. Sitting on the throne, surrounded with Byzantine decorations.
Spoiler :
I hoping her personal traits would be seductive and cunning