@libbyrose1014,
When I read your post, the Barbra Streisand movie, 'Yentl', immediately came to mind.
http://en.wikipedia.org/wiki/Yentl_(film)
I don't know if you have seen the film, which is based on Isaac Bashevis Singer's short story, "Yentl the Yeshiva Boy". In both Singer's story, and Streisand's film, Yentl is an Ashkenazi Jewish girl living in an Orthodox Jewish shtetl in Poland in the early part of the 20th century. She fervently wishes to study the Torah, and pursue that type of scholarly life--something that females, in that time and place, were not permitted to do, by deeply entrenched religious tradition that defined gender roles. So, in order to fulfill her goals, and her own self fulfillment, Yentl undertakes the subterfuge of assuming the name of her deceased brother, and taking on a male identity.
The Streisand film takes a more feminist and positive view of Yentl--her attempts to fight against religiously imposed restrictive gender roles, and the lengths she goes through to conceal her female identity, in order to achieve her personal goals, are seen as virtues and strengths we can admire. At the end of the film, she decides to go to America, a place she feels will offer her more personal freedom.
In the original Singer short story, which I have not yet read, the outcome for Yentl is apparently less optimistic and rosy--she becomes doomed to wander around, fitting in nowhere, living a life of pain and alienation.
I did not feel angry at the female's situation, and her need for the male subterfuge in the film, although I could feel sadness that a woman, in that time and place, would have to resort to concealing her female identity in order to do what any male in her community was able to do as part of his birthright
So, at least in terms of that film, as a female, I didn't have the double edged reaction to this sort of scenario that you do. I admired the character's ingenuity and determination--I could empathize with her wanting to pursue her own goals, and I could accept her need to appear to be male in order to be able to do that. And, in the long run, her ultimate solution would have to involve removing herself from the restrictive and confining world she was living in, if she could, and moving to a country where she would find greater personal freedom, which would also be a gutsy and brave move.
So I definitely feel you could write a story that would be considerably more empowering than offensive, even set in the present, depending on whether you create a female character who can be admired for her strength, courage, and ingenuity, and who has a compelling and realistic need to cross-dress as a male. If you focus on her positive attributes, and her ability to meet challenges, without undue resentment or anger about her need for cross-dressing, I think you can achieve that.