As long as you do your research and treat the subject with respect, there's no reason why you can't write about it. I imagine homophobia in the 40s was very different than it is now, and homophobia towards lesbians was probably different than homophobia towards gays. If possible, I highly encourage you to try and find a primary source - maybe try to interview an older lesbian woman, or find someone whose late mother was lesbian in those times. If you can't interview a person, try to find a journal or a memoir or a biography from around that era.
Especially with historical fiction, getting the details right can be very important in writing a successfully believable story. A lot of writing tends to be making things up, but with historical fiction you really do need a solid basis of the reality of the times first. And if you do find a journal or biography of a lesbian woman from the 40s you obviously don't need to or shouldn't just translate her life into your character for your comic, but it may open your eyes to experiences that you didn't know a lesbian in that era would have gone through, or what the attitude towards lesbians was at the time that may be different than what is currently in your head.
The whole "you can't write X if you aren't X" thing that goes around is a bit of a fallacy and a bit of an extremist statement. Of course it is possible for a white man to write a story about a black woman and do it well if he does his research, but a black woman writing a story about a black woman may have more correct nuances to the character and their lives, and the situations she writes from will be from personal first-hand experience of her actual life as a black woman rather than just her imagination of what a white man thinks a black woman experiences, which can lend a bit more believability and delicacy to the character.
I firmly believe that anyone can write anything as long as the subject is thoroughly researched, handled tastefully, and treated with respect.