The First Amendment specifically prohibits the enacting of laws that would favor one religion or prevent the freedom of an individual to believe in and express their religious views.
Given the above, there is nothing illegal or morally wrong with a Christian prayer being conducted before a governmental activity. There is no one stating that only Christians can attend council meetings or that non-Christians must bow their heads and accept the prayer being given. While it might, perhaps, violate Jefferson's wall between Church and State, his words were merely a written opinion and not a law.
Personally, I'm an Agnostic (an Empirical/Weak Agnostic, if there are those who require specifics). While I might not hold the beliefs of those conducting the prayers, I feel a certain amount respect for their personal beliefs and convictions. That is more what this whole debacle seems to be about... respecting the beliefs of others or denying them their practices out of a lack of respect. As far as I've noticed, the City Council has not stated that only Christian prayers may be spoken before a meeting or that attendees must believe and pray as they do. Rather, this situation arose from a single attendee who, rather than voicing their opinion at the meeting, chose to keep quiet until they were 'safely' away and then threatened with law suits... threatened, mind you, to prevent the free exercise of religion by another citizen.
It might be hard for some non-Christians to swallow (or, in this case, more radical non-religious individuals), but it is quite possible to sit through a prayer and feel no offense. I don't believe in Christ (as the son of God, rather...I do believe he was an important historical figure); however, when one of my closest friends, a devout Lutheran, prays before meals, I will sit and remain silent as a matter of respect for his chosen beliefs. I do that because all I ask of others is to respect my beliefs and convictions.
Let's look at it from a different perspective. Prayer, at it's most basic and without the religious aspects, is a meditative state. It helps individuals to focus their minds on a task at hand or provides a moment for the release of tension. Personally, as it appears all of our council members are Christians, I would rather they experience less stress and a bit more clarity of mind before they proceed to make decisions that affect our city. It's their religion, their prayer and it helps them in some way. If it isn't your religion and you happen to be attending, remain silent during their prayer then ask if you can offer a "prayer" of your own.
Another issue with demanding they remove prayer or prohibit these individuals from praying in the name of their God(s), you open the door to them using the same arguments to deny or prohibit your practices. If this same inividual who sent the email comes forward and starts to state their beliefs in an open forum, they can now, effectively, be told they cannot do that... by their own argument that it may be offensive to a single person attending. Sadly, that is the way we are going... and, honestly, it isn't the "Christian Right" that's accomplishing the task; rather, it's the individuals taking offense at every act of religious bodies.
We need to get away from the "rights of religious expression" and head towards respecting the beliefs of others and allowing them to express them, even if we don't agree with those beliefs. Honestly, if you want someone to respect your personal set of beliefs, you have to offer that same respect in return.