First of all baring swearing or abusive language and some possible other exceptions teachers cant control what kids say. Especially religious or political speech within reason (Could still move into the abusive spectrum). Rightly so as this is protected speech.
Second "Bless you" isnt a christian saying it may have religious roots but it said by a wide verity of people (including me an atheist) in response to a sneeze. She also had a list of other phrases that were bannd and this is the only one with any religious connotation and from what it seams. This is hardly any evidence of a far reaching anti-christian conspiracy. Like the story said it may have been causing a distraction and by that i mean kids may have been yelling it really loud across the room at each other. Having been in high school i'm sure we all know kids do whacky stuff like that to annoy teachers we don't like. On the flip side if the teacher was trying to ban religious speech on the basis of she does not like it. Then she needs to be disciplined. Just like what happens when Christian teachers abuse their power and force their beliefs on their class although in the bible belt it takes allot to of courage to speak out against it as its way more common.
Christians are a majority in the US and their idea of persecution is when people call them out for giving their faith special privileges. For example Christian only invocations at town meetings, Ten commandments displays at court houses, school lead prayer, religious based banners in secular schools... the list goes on. Stop screaming persecution when you are the most privileged majority. Governments and their employes (including teachers) on all levels should be secular (in their official dealings) because it promotes true freedom of speech and religion and puts all the religions and expressions of non-religious on the same footing and under the same protections.