While it would be easier for the students to be separated by some of those characteristics in the short term, it would make things more difficult for them and society as a whole in the long term. If boys and girls (or black students and white students, etc.) don't learn how to work alongside one-another when they're young, then they're going to have to go through those struggles when they're older--either in college or in the workplace--unless you're advocating for completely apartheid society.

Such a society may be plausible with regard to race (though I'd contest the notion that it's desirable), but it's certainly not plausible with regard to sex. As for sexual orientation... even just separating schoolchildren on that basis isn't really possible, since kids often can't confidently classify their sexual orientation until their mid teens.

I don't think your solution would actually solve the problem you're seeking to address, either. Segregated schools (or societies) would probably result in an increase in disparities between groups, since the separation allows bigoted actors to more easily target members of certain demographic groups for mistreatment. It would also enable curricula and educational styles that reinforced problematic racial stereotypes, gender roles, etc., making integration down the line even more difficult.

Speaking of which, are you proposing that the education system would remain divided these ways indefinitely, or just until some standard of equal treatment in integrated schools could be assured? If the latter, then what would that standard be? If the former, then why do you believe that equal treatment can never be possible?

P.S.: Speaking in generalized terms about some demographic group doing some bad thing is unhelpful, inflammatory, and typically leverages its vagueness to try to support some sort of incorrect conclusion--and in case you're wondering, I say the same thing to white people making unflattering generalizations about a black person, men making unflattering generalizations about women, etc.