Where I work, a local minister always recites an invocation before every City Council meeting. The Mayor requests that everybody stand for the invocation. At the meetings I've attended, the invocations aren't short prayers; they approach the 90 second to two minute mark. The prayers also aren't generic, appealing to God or "a higher power" in general; they're specifically very Christian, mentioning Jesus. The last prayer was uber-Christian, with one line being "Jesus, pour your blood on City Council and city staff".
If City Council wants to pray, it's fine by me, even though the courts consider it questionable. However, being Jewish, I'm not exactly comfortable with standing up and praying to Jesus. Jesus was a great guy and all, and I appreciate that people want to give props to a fellow Member of the Tribe, but still ... you know. Anyhow, being a new employee, I don't want to make waves, or be seen as one of "those Jews" who's trying to spoil everyone else's fun. (FWIW, I'm Reform.)
Do you think it would be appropriate to stay seated during the invocation, and then rise for the Pledge of Allegiance afterward? I'd be the only one that would be seated. I think I'm the only Jewish city employee, and the city is quite far from the center of the region's Jewish community; I'd say the population of religious adherents that are not Christian there is close to zero. I'd prefer not to strategically show up late, or wait outside the chambers and time my entrance just before the pledge, but I'll consider doing so if it's the only way to avoid public prayer.
FWIW, I've never been preached or proselytized to, not experienced any other problems because of my faith. Please don't ask where I work; I don't want to see the city get in trouble over this.