Simply that human nature doesn't change that quickly and the separate facilities will soon be funded inequitably because of that.
Separate facilities are already funded inequitably because of the way school funding works in most areas.
By this logic of "It didn't work out like the theoretical model and still has a lot of inequality, so we should ban it" we should ban non-segregated schools I guess. Maybe ban public schools in general? I don't know. The logic of making something illegal because it didn't work as expected just doesn't make sense. It can work in principle, that's what counts.
If you're worried about a situation where public officials start making boys schools really awesome and girls schools really bad, then make THAT illegal. Put mechanisms in place to protect against THAT. Do you think that can't be done for some reason?
Show me any time in the past where that hasn't happened instead.
I know plenty of gender-segregated schools that seem to work out pretty well.
Gender-segregation was explicitly carved out as an exception to anti-discrimination laws. "If a private school gets federal funding, it can’t discriminate against a student based on his race, sex (unless it’s a single-sex school), national origin and religion."
There are plenty of single-sex schools that A) operate legally and B) even get federal money.
So clearly segregation works and is seen as "ok" in some cases.