not exactly! Female crossdressers have been historically tolerated- even encouraged- since it was seen as them aspiring to be better, to be men. The Germanic laws against crossdressing that made it an actual crime were phased out pretty early on in the middle ages- and even then men were persecuted far more often than women were.
preeeeetty sure they were trying to politically silence her by calling her out for heresy. There wasn't a witch hunt for Joan just because she was wearing men's clothing- it was used as an excuse to persecute her.
Another magnificent Harley redesign from you. I like it a lot, and it's even more appropriate to me than Queen Harley--although that one was also great. This is just even better than that, in terms of fitting with her character.
I hope that you are inspired to do a Joker companion piece sometime, although I'm aware that you've probably gotten similar comments approximately one bajillion times already.