Tzipporah had also converted. Moshe got very angry with the soldiers who brought back Gentile women (BaMidbar 31:14-15) Wouldn't that have been pretty contradictory on his part if Tzipporah was considered a Gentile herself?? Of course it would. She also had converted and was no longer seen as Gentile. They were Jewish..that is WHY the children were to be circumcised...obviously. Do you find Hashem instructing non-Jews to be circumcised? No. They are only to circumcise their males if they wish to convert and come into the Covenant between Hashem and Yisrael...and by doing so they become 'Jewish.' Tzipporah kept the mitzvah of circumcision because she was Jewish.