This is more like a general principle I like, and it's not necessarily going to be possible for you in this particular case, but still something to keep in mind:
If possible, let the player make the choice through gameplay. For example, maybe the choice can be presented at the end of the previous mission in the form of which jumpnode to use or which carrier to land on. Or, the mission simply starts with protection of the planetary evacuation and very soon the information about the convoy comes in and you have to choose whether to engage your jumpdrive to abandon the evacuation and go save the convoy instead. Or maybe both the evacuation and the convoy are physically in the same mission but far enough apart that it's impossible to succeed in securing both.
As said, maybe not something you'd want to do in this particular case, and there's nothing wrong as such with presenting the choice explicitly in the interface, but sometimes gameplay-driven choices are a bit more immersive and exciting, especially on the first playthrough.