If the Naval Progression mission tells you to do an assassination, then you will have to. If you are just talking about gaining rep to be offered a Naval Progression mission then no, doing other missions to gain rep is just as good. If I remember correctly I did have to do one assassination mission on my way to Baron, but I don't know if that was just by luck of the draw or that everyone has the same missions.
You might have to just try it when it comes around, making sure you have the strongest ship you can afford with money for insurance. If it's going badly you could just run and retry. You get at least a day to complete the mission, and even if the time runs out you can keep repping up until you get offered it again.