My main concern is that the kids will miss out on a significant part of the intergender socialisation process that usually occurs in mixed-gender school environments. Even if they're allowed to mix outside of the classroom, a lot of interaction occurs in classrooms, and isolating the genders in separate classrooms may have a knock on effect of reducing interactions outside of the classroom due to reduced familiarity between individuals in each group. School should be as much about producing socially balanced individuals as it should be about the pursuit of academics.
It's good that they're making an effort, at least. When I was in primary school, it was just industrial-scale, government-run daycare, and nobody gave a shit about whether or not we learned anything or ended up well adjusted. Mostly, they just plonked maths books in front of us and made us do maths exercises for hour after hour. I used to like the occasional English lesson, since anything was better than more fucking maths exercises. I didn't even get a science or foreign language lesson until year 7 (age 12), right before I went to secondary school, and those were just one-off lessons from a couple of teachers that visited the school for the purpose. I also didn't become a maths genius, which would at least have been some consolation.