"By the "tolerance" line of reasoning, citizens of Northern states should have kept their big mouths shut instead of complaining about Jim Crow laws in the South."

Sorry, Aaron, that's a flawed analogy.  The Jim Crow laws were imposed by the governments of Southern states, and blacks (or non-blacks) who were unhappy with them had no alternative but to relocate to the Northern states, which would of course have been economically unfeasible for many if not most.

The separation of women and men in Orthodox shuls, while again I share your disagreement with the concept, is not the same thing.  The Orthodox Jews, in the Diaspora, are not the government.  They cannot force all Jews to worship in their synagogues.  Since the nineteenth century (and from the beginning in the U.S.), Western Jews no longer live as non-citizens governed by local, semi-autonomous rabbinical courts with the power to enforce halakhic observance.  There is no comparison between today's Orthodox community and legal, systemic discrimination against blacks.

A postscript:  when I was young, before I had actually gotten to know any Orthodox Jews first-hand, I imagined that Orthodox women felt so, so terribly oppressed by their male overlords.  When I entered university and started hanging out at Hillel, I asked many Orthodox women, when there weren't any Orthodox men within hearing, questions like,  "Don't you wish you could be rabbis?  or cantors?  or do this or that?"  Their answer was invariably,  "No.  Why should we?"  Now you could counter that they've been "brainwashed" or other hyperbolic terms that dilute the meaning of real brainwashing.  I call it their cultural upbringing, just as we egalitarians have ours.  If an Orthodox woman, upon reaching maturity, decides she doesn't like the system in which she was raised, she's free to leave it.  In some cases, particularly with secular-education-poor haredim, there may be sacrifices and hardships ahead, but she still has the choice.  Rabbinical courts no longer have the power to fine or flog dissenters.  And they've never had the power to imprison them.

I maintain my stance:  if we don't like Orthodox Jews lecturing us (and in the Diaspora they do no more than that) on how to practice Judaism, we shouldn't do the same to them.  Tolerance works both ways.  That's all I have to say on this matter, thanks.