I would disagree with @user6726 somewhat on the application of the legal standard to these facts even though I don't think that we disagree much on the applicable legal standard.
If a church venue is used simply because it has a large auditorium space and the program has no religious content, the mere fact that the program is conducted in a church does not violate the establishment clause. The program has to promote or condemn religion to constitute an establishment clause violation. While it is easy to imagine a field trip to a church that does promote religion, the field trip in the question shows no sign of having that purpose.
A speculation that there is an improper motive to make students comfortable with a church setting to encourage them to convert, as the question suggests, without any solid evidence to back up that inference, is not likely to prevail in court.
Along the same lines, a field trip to a baseball stadium does not violate the establishment clause of the First Amendment simply because on Sundays mornings, a local megachurch conducts its worship services there.