So, if he has to choose between his religion and the charter school are his civil rights being violated?
Not in any sane world. Because it’s not a public school and not run by the government and the association they have between them is totally voluntary they don’t have to respect his religious views. He can keep his hair long, he just has to go to a different school to do it. Private parties engaged in voluntary interactions cannot violate each others civil rights, they just need to be smart enough to know when they are at cross purposes with one another and need to end their association.
I don't know. The school's strict dress code is based on getting the students used to a business environment, or so it says. Of course, business dress codes are also becoming more lax, but would an employer be as likely to hire a man wearing a bun as one with close-cropped hair? And would the employer tell the prospective employee why he had not been chosen?
Also, it's not as if the student has to choose between his religion and attending school - as discostu points out, there are other public schools open to the student that would not object to his hairstyle.
Finally, the school states that they were trying to verify that the religious objection actually exists. It sounded as if they were open to granting the student an exemption, IF he could prove his point.