I think she should have helped Jake capture Tom, instead of letting Jake kill him or let him get away with the cube.
Rachel most likely would have lived, and possibly the Auxilaries. Remember when Marco said they had trouble in the pool ship. There were so many enemies to get past, and who do we know that's good at barreling through enemies? Rachel being on the pool ship at the time may have helped a lot. Unfortunately, she was on the blade ship because of Tom and the cube.
I've gone though it all in the thread Cassie's Betrayal, so I may not say much more than this.