I'm not too sold on Cerberus either. ME3 kind of turned them into cartoon supervillains, which is not inherently a bad thing, but I can't really take them seriously in ME anymore. Even if that whole "...and then it turned on them and started killing their dudes." conversation in ME3 was amusing. Because, really... That's what they do. Repeatedly.
Still, having Cerberus sympathizers on the ark could be fun, or if they want to keep it on the cartoon supervillain level, they have their own ark, which for some reason arrives in the same area of space as yours. It would, at least, be worth it to have a plot development where you think you're making first contact with an alien species, only to have them react aggressively since the first humans they saw were monsters. Then you have to track down whoever that is and beat them up.