The big issue, which I do not know if you understood, is that we do not know the motivations behind the Empress' actions. In the absence of a direct and undisputed quote from the Empress indicating she was a Monophysite, or without being found guilty of Monophysitism by the Church, to declare her a Monophysite is incorrect.
The problem with using the M-word is that its application is vague. In this forum, it's supposed to be used only for Eutychians or Apollonarians. However, a lot of people use it pejoratively to refer to anyone who rejects Chalcedon, including the OO's.
I truly doubt that the book Alexios is referring to is specifically making the allegation that St. Theodora was a Eutychian or Apollonarian. I've just never heard anyone make that allegation. The author is probably using the M-word in the second, more vague and pejorative, fashion. That has been my experience in reading about St. Theodora. The people who use that word for her will also use it against St. Severus, and he explicitly condemned Eutyches and Apollonarius.
It would be nice if Alexios could check the book and see if the author uses that word to describe not only St. Theodora, but also Severus of Antioch. If that is the case, then he is using it to describe anyone who doesn't accept Chalcedon. I strongly suspect that is the case.
So the question is really whether St. Theodora was a Chalcedonian or a Non-Chalcedonian (OO.) My belief, and I think the belief of most people, is that she was Non-Chalcedonian. This is for the following reasons:
1. People who were contemporaries of her described her as such. I am aware of no contemporaries of the saint who claim she was a Chalcedonian who was merely doing pastoral outreach to Non-Chalcedonians. To the limited extent that I have read anything that viewed her as Chalcedonian, they were sources written centuries after her death. They seem to be polemics aimed at denying that anyone venerated by EO's or Catholics could ever be a Non-Chalcedonian.
2. The things she did for the Non-Chalcedonians went way beyond what could be viewed as Chalcedonian pastoral outreach to Non-Chalcedonians. She hid Non-Chalcedonian theologians and bishops from her husband, when he wanted to arrest them. She sent out Non-Chalcedonian missionaries, and I have heard the story mentioned by Alexios, wherein she delayed Chalcedonian missionaries so that her own Non-Chalcedonian ones could reach their destination first. Those are just not the actions of a devout Chalcedonian, regardless of what her pastoral duties may have been.
With regard to Chalcedonian polemics aimed at spinning history to make St. Theodora seem like a Chalcedonian, it's not like there aren't any OO's who are guilty of this themselves. See reply 46 in the above linked thread, which I'll link again:http://www.orthodoxchristianity.net/forum/index.php/topic,10408.msg150810.html#msg150810
This is an example of an OO who just can't accept that the OO Churches venerate a saint who was probably a Chalcedonian (St. Simeon Stylites.) It just hurts some people to think that the "other side" could have some people who are worthy of veneration.
The reality is, however, that the OO's venerate at least a few Chalcedonian saints, and the EO's have at least one saint (St. Theodora,) who almost certainly was Non-Chalcedonian. The polemicists need to just accept it and get over it.
I know you are uncomfortable about St. Theodora's possible affiliation and some of her actions. She is, nevertheless, a saint worthy of admiration, respect and veneration. Her love for Christ and her piety are unquestionable. She may not have supported her husband's religious policies, but she supported him in all other things, and was responsible for him surviving a horrible political revolt. She was, in the end, a faithful and loving wife.