Maybe I'm biased and need to look at the SSA rankings, but Margaret doesn't strike me as "old lady trendy" quite the way, say, Violet or Hazel do.
I feel like there is a sharp divide between grandparents with the old lady trendy names, middle generation with almost none of these names, and now young children bearing these names. However, in my family, my grandmother, my great aunt and my mother all are named Margaret so it feels more timeless and less trendy to me. The numbers, however, may prove me wrong.
So, on that front, I'd encourage just using Margaret since you've loved it for so long. I understand how you feel about wanting people to know that you are a historian and didn't just jump on the old lady trendy bandwagon.
I do love Magdalena, though. Different. More unpopular. It does, however, give off (at least to me) a distinctly biblical vibe which might not be the history connotation you are going for.