You're mixing up three things here.

(1) To what extent, and in what direction, the school (and others) should defer to individual beliefs (whether Mr. Burke's or a student's)

(2) Whether it is reasonable, appropriate, or legal to show up somewhere you are not authorized to be (as opposed to, say, adjacent to there)

(3) Whether the whole episode was manufactured by the school's lack of clarity

You can, for instance, believe that Mr. Burke has every right to use whichever pronouns he wants for whomever he wants (especially if it is a matter of religious belief) and that if the school has an injunction against him actually entering their property that it is entirely reasonable that he be jailed if he fails to comply. This would actually be a pretty sensible thing to believe: civil disobedience done in an illegal fashion makes for a particularly striking statement, but one also should not expect to avoid the legal consequences. What makes it striking is the presumption that the participants find the moral call to do it outweighs the practical disadvantages, but this does not mean that we just suspend laws willy-nilly whenever someone feels strongly.

If you write your headline as, "Suspended teacher trespasses repeatedly on school grounds, is eventually jailed," it seems like...yeah...that part's working out exactly the way it's supposed to. He wasn't jailed for his beliefs. He was jailed for the extreme actions that his beliefs led him to.