This is my main concern in regards to mentioning specific sectarian prayers. As an atheist, I take the high road in regards to the general "God" in prayer - I recognize tradition in that sense and I don't get butt-hurt with this fiction. But, I know the people who are most energetic in regards to these prayers will be the first to fight any mention of Allah or other non-Jesus counterpart.
Yes, many just see it as part of their heritage. So, rejecting it is like rejecting their country, family and history. It becomes un-American.
My brain realizes that ultimately, the best answer would be a non-religious statement, like "We the people..." in place of Gods. But, my heart realizes that the culture isn't there yet. I would hope that they would at least use general prayers and recognize that other religious people get just as butt-hurt as they do in regards to their favorite stories.
It is a form of peer-pressure, so I do think its an important issue, but pragmatically, it isn't a battle worth fighting at the moment, IMO