Travel agents in the United States generally supply people going to the Holy Land with set tours and often they assume that you will want to go on that same standardized tour. Itineraries are chosen with general tourists in mind and the choice of sites will reflect someone else's choices of what is important. But you are opting for another kind of trip. The point is you have to ask for other experiences and you might even have to supply some examples.
Do not be put off by excuses such as safety or lack of time or lack of contacts. Since you are paying for the trip, you have the right to expect the trip to satisfy your group's needs. If not, find another travel agent. In this time, though, check safety issues with someone from a church or agency.
The USA travel agent can work with a Palestinian travel agent on the details. Some of these agents are Christians themselves and know the possibilities. Or you can work directly with a Palestinian travel agent. Email means that you avoid long distance phone calls.
In planning the itinerary, be clear with the travel agent or other contact that you want to go to church on Sunday and don't schedule a long trip for that same day. Schedule speakers during the day as well as in the evening and don't schedule one at the end of a very busy day. The tired travelers won't pay attention.
Include stops at "fair trade" stores where the craft workers are paid a fair wage and where no one makes a big profit from the sales. Since there is high unemployment in the West Bank and Gaza, whole families are sometimes dependent on the income from craft work done in the home.
Request hotels or hostels owned by Palestinian Christians. The Palestinian economy needs all the help it can get and there are many fine hotels in East Jerusalem.
Breakfast comes with the overnight but don't let your travel agent schedule all dinners in the hotel. There are also excellent restaurants that are not too expensive and give you a taste of local fare. Never take full board where you have to return to the hotel for lunch.
Ask for a Christian guide. Because of a deliberate policy decision by the Israeli Ministry of Tourism over 20 years ago to limit the number of Palestinian Christian and Muslim guides, there are only a few available. Your request helps create the demand. In the training of Israeli guides, very few hours are spent on Christian sites and Christian understanding so there is no standard for knowledge of Christianity. Several West Bank institutions are training Palestinian guides but there are still problems in licensing for travel outside of the West Bank. This may change in the future but it will only change if travelers ask for Christian guides.