The Glory is an amazing ship! I was on it a few years ago, and absolutely loved it. I am not really familiar with the tours the ship is giving, but I visited those ports last year with RCI explorer. If you want full access to Atlantis, then I would go with the tour, but my family, instead of paying for a tour, took a taxi to atlantis, and walked around the resort for free. After walking through most of the resort, we only then realized signs saying, 'guest only area' but no one said anything to us, and we were just looking, so, if your just want to walk aroung Atlantis, you can really do that for free.
Magens bay in st. thomas was enjoyable. I love white sandy beaches, and this was a nice one. My family enjoys snorkeling, and to the far side of Magens bay is a little rocky area that my family said had lots of fish.
In st. maarten, we took a tour of the island and that tour took us to orient bay beach, which was really nice too. Hope some of this helps!