Essay page by User:GRuban.
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These questions seem to come in opposing pairs; it seems our article has successfully hit the middle of two extremes.
Q1: Is the existence of this article promoting a violent criminal?
We don't write articles to promote or reject their subjects, we write about people and topics that are Wikipedia:Notable—"those that have gained sufficiently significant attention by the world at large and over a period of time." Baker has received that attention. We have many articles about much worse people.
Q2: So, shouldn't we focus on Baker's activism since her imprisonment?
We write from Wikipedia:Neutral point of view, which means "representing fairly, proportionately, and without editorial bias, all the significant views that have been published by reliable sources on a topic." Baker's crimes received significant coverage, so we need to proportionately reflect that.
Q3: Should we use male pronouns to describe Baker, especially before her gender transition? Writing about her raping a man, engendering a child, or cutting off her testicles is confusing, and Baker was called "he" during those events.
We have to follow Wikipedia:Manual of Style/Biography#Gender identity, which means to "Refer to any person ... with the name and gendered words ... that reflect the person's most recent expressed self-identification as reported in the most recent reliable sources, even if it does not match what is most common in sources. This holds for any phase of the person's life, unless they have indicated a preference otherwise." We do try to use less surprising wording wherever possible, except when that would lead to leaving out important information.
Q4: Then shouldn't we exclude Baker's birth name, and otherwise not focus on her life before her gender transition?
As in Q2, we write about the subject proportionately to their coverage in reliable sources. Baker was the subject of numerous articles from reliable sources before her gender transition, and published an internationally reviewed book under her birth name; so as in Q3 and Wikipedia:Manual of Style/Biography#Gender identity, we do include limited (two) uses of her birth name where they are important because she was notable under that name. Throughout most of the article, we refer to her by her surname, which avoids the issue.
Q5: Since we focus on reliable sources, should we remove the citations to the articles from the Daily Mail (and the Daily Mirror) which are not reliable per WP:DAILYMAIL?
The two Daily Mail and Daily Mirror articles stating Baker transitioned at government expense are not only not reliable, they are outright false, as the article says. The articles are not being used as sources, they are being used because they are the subject of the discussion; that is specifically what is called out in WP:DAILYMAIL as "The Daily Mail may be used in rare cases in an about-self fashion."
Q6: So shouldn't we have more content from the Daily Mail, Daily Mirror, Sun, and other British tabloids, which write extensively about Baker? Especially since Baker herself says she wanted to be written about in the Daily Mail?
As per Q5, we do not use tabloid sources for information about living people. Even if those living people like it.