It is hard to believe that even Islamic schools teach kufr. You might be exaggerating a bit. If conventional schools teach kufr and one is afraid for his Iman, he must not go to these school as and must get home schooling instead.

Is attending a school that teach kufr, permissible. That school teaches you to question everthing also, is that permissible? Will I become a kaafir if I attend that school? All the public schools teach kufr in canada, and even the full time islamic school.