Those are both excellent points. Whatever meditative benefits prayer might have as a function of religion, it's not an educational tool, and any attempt to use it as such in a publicly funded setting is a clear violation of The Establishment Clause or Equal Representation depending on which way you want to look at it.
Frankly, the privileged treatment of religious organizations is what really gets my goat in this country. I attended Episcopal parishes well into young adult hood, which provided community, friendship, progressive moral grounding (that is to say, not indoctrination along dogmatic lines) and had a lot of fun doing it. The church provided resources for not just people like me, but supported the community food banks, ran a soup kitchen, hosted AA and Narcotics Anonymous meetings, and provided training to lay-persons to become caregivers throughout the community. For all that, they enjoy tax exempt status and don't really tread on anyone's toes.
Then I look at the local evangelical mega church which directs it's funding towards trying to influence school board policy, buy local elections and picket planned parenthood clinics. I've tried attending a few of their services, where they have surround sound, big screen displays and a praise-music band of over the hill rock-a-billies, and their youth group center has it's own set of flat screens and x-boxes and for-proft snack bar. For all that, they enjoy exactly the same tax exempt status, and they're not even the worst offenders by a long shot.
Why don't the same rules that apply to most not-for-profit organizations apply to churches as a whole? When the director of a planned giving organization starts lining his own pockets and letting his inner circle enjoy gross company perks, he can be held accountable. When priests do the same thing, it's almost impossible to nail them on the same kind of fraud, simply because they're "Men of God" (whether or not they actually have any kind of theological background).