This has been very interesting for me to read, as my son is right now, at this very moment, away on a youth retreat.
If he returned with the news you mentioned, I would be very unhappy. I agree with your words - Danger! Danger! Danger!
If this was an unavoidable situation at the hotel, then an adult female should have stayed with them. No two ways about it. Or, they should have been put up on the floor with the rest of the group and boys with a male leader could have stayed in that room.
The safety of the young people is first. Period!
I think the only young people I would have considered putting in such a situation would be much older high school kids - such as juniors or seniors who had a known record for being very responsible kids. Afterall, a high school senior is just about ready to go off to college anyway. But I still wouldn't be happy with even them be separated off from the group. They go away to be together.
They are immature by the nature of their ages. I assume they came home alright, but what if they had made a bad decision, such as opening the door to a stranger, or leaving the room and encountering problematic hotel guests? Who was there to protect them from making a bad decision?
I'm not sure who I'd speak with, many churches have different types of chains of command, so to speak. Are other parents upset as well? I would think there may be parents at your church who would be upset even if it wasn't their own child.
I think I would approach this in a united way and together. Does you church have a set of regulations or rules about how things are handled with regards to youth events? (FYI - around here, you can't work with the youth unless you've had a criminal background check, so things are very strict.) If you don't have rules to cover situations such as this, perhaps this is something really good that can come out of the situation - a guidebook on youth events and so forth.
I would be hesitant to send my child on another retreat unless I had been assured this problem had been ironed out.
Hopefully your church will be very open to working this out with you. Don't forget, you are the parents and it's up to you to turn your authority over to people who will behave with responsibility. Ultimately, YOU are responsible to God for your children.
God Bless you.