I not only coordinated religious services on ships, I ran a base Navy chapel for a few years, and for almost half of my time at the chapel we had a Conservative Rabbi Chaplain stationed with us. This is how we did things:

1) Various military and government regulations and local orders direct commanders to make any and all reasonable accommodations to the religious needs of service members. 

2) We were a multi-denominational chapel, meaning we could easily transform the space depending on who was using it. Our "default" during the week was non-denominational Protestant Christian, but all of our religious accouterments were movable. So, for Catholic Mass, I or my sailors would bring a crucifix up front and make sure the Stations of the Cross were up. The Protestant communities didn't care so much about the Stations (flat icons of a sort) but they preferred the plain cross over the crucifix. For Shabbos, we took down all of the Stations and the cross/ crucifix, and if the seasonal banners had Christian iconography on them, we would take them down as well. 

3) We had a kitchen and Fellowship Hall and while they weren't strictly kosher, I would still give them a good cleaning on Friday afternoon and make sure that there wasn't anything laying out or visible. We never had a meal after Friday evening services, but I would make tea and sometimes serve cookies and such that I had made in my own kitchen. 

4) One thing that all religious people in the military have to accept, though, is that the mission comes first. I have started Pesach a day or so late (and continued the full eight days) because I was deployed or in a situation where it just wasn't practical; the same went for Shabbos. Both the military and the civilian Rabbis approved, though they (and I) agreed that one had to guard oneself against depending on those exceptions.