I'm actually going to use this bit of dialogue for an upcoming mission of mine.

"sir, although we go where you order us, I would suggest leaving us to guard (insert whatever you want, transport site, doorway)"

Then to compete the injustice of your crew abandoning you, once you reach a point have imaginary walls sprout up blocking them in or if an indoor map, a good force field in a hallway.

If you do want the player to set a rally point, be sure to tell them how to do it. Not everyone knows how, especially if they are new to the game.

Here's my sample text for describing the process: How To Set A Rally Point

I hope they knew how when they played the breen missions. Your point is well taken, and since my mission for the challenge has such a part in it, do you mind if I paraphrase the second paragraph?