That is neither an unknown or uncomfortable situation.
Bolded: Speaking only for myself, it's more that allowing prayer is the government "establishing state religion". It's not that it's Wiccan, Islam, FSM, Christianity <shudder>

, etc., it's that it's a government stance of "religion: positive" vs. "religion: neutral". I'm not discounting at all the value religion can have on an individual and even societal basis, nor am I holding a mirror up to religion(s) and saying "look at all the bad you've done and continue to do".
Adherents of all faiths or none are better served by a secular government that tolerates no shenanigans by it's members, however well-intentioned or sincerely meant.