The Sensei has to make a decision, is he interested in accepting all interested students, or is he going to discriminate against those for whom the Dojo rules must change?

Any decision is legitimate. But please, be honest, if you insist a student must transgress basic rules of his religion, you may as well ask him to change religion. This type of requirement is discriminatory.

I guess many here miss the importance of sex segregation in Orthodox Judaism and Islam due to your living and being brought up in a Protestant Christian environment (or a secular post Protestant Christian environment). I do not know of equivalent fundamental rules in Christianity. Though I am sure there are some. Growing in a secular post Jewish community, I find a huge distinction between the Orthodox Judaism concept of opposite sexes segregation and discrimination against women.

This might be the legal side. Yet, this is discriminatory in the moral sense.

True, but are all the rules equally important?

Sorry, but this example is misleading. You compare a person with no respect to tradition, to a person who follows one tradition and is interested in practicing and honoring another.

I agree, this does make a poor training environment. Yet, not traveling and not turning the lights on one day a week seems much more harmful of life quality, and religious Jews do it one full day (>24 hours) every week.

The difference is the matter of cause\motive. If one is dismissive of other peoples, and a racist, you are right. But if one only follows his religion, and is willing to do the most his religion allows him to, it is not the same.

WE respect Japanese tradition while practicing Aikido, are we bound to disrespect any other tradition (most of which pre-date Aikido by many hundreds of years)? Can one not find a way to respect both?

Ahmed never said men and women are not equal, this is your interpretation.
I do not know his explanation (the Islamic one), but for instance some Orthodox Jew interpretations I have heard would believe that the woman is more worthy, and her honor should therefore be kept inside.
Ahmed (and many religious Islamic and Jews) may train with women -- these are the rules of his religion -- you can either accept him or discriminate against him, period.
Actually Religious Jews are only allowed to touch women, after both have gone to purify in the Mikve (special water pool), are you willing to create on in your dojo and ask all women and men to go there prior to training?

Amir