It's interesting b/c on one hand the doctor is the "feminine" animus which acts as moral conscience, as pacifist, as priest/healer. A respect for life as end in itself. Whereas Jack is male animus, dominating and in a pursuit of excellence. The doctor heals what is broken, and the captain breaks; the doctor is always responding whereas the captain must take the initiative, force the enemy to respond or else he's on the losing side. (The first two encounters between ships, he's forced to respond; the second encounter, he changes the balance of power.)
On the other hand, the doctor is a scientist, a cataloger and classifier of the world, which is a very male impulse. So in some sense, it's two male archetypes, the scientist and the warrior, the observer and the actor, pursuit of knowledge and defense of country. And yet the film tells us that each is bound to the other—the doctor takes up arms, the captain acknowledges the value of the Galapagos expedition. You defend country so that you can do things like art and science; they're what you're fight for.
Very similar archetypal stuff happening in Farscape. John is a scientist who is gradually forced to take up arms to defend those he loves, even as he resists its necessity. Aeryn is a warrior who realizes that all the control and violence is wasted if it isn't to protect love, to protect people you care about. And then Zhaan and D'Argo are their extensions—Zhaan is a scientist who has fled a violent past and is terrified by/haunted by the prospect of her own power, and the havoc it can wreak; D'Argo is a warrior driven mad by love, who is always up against roid rage/anger mgmt problems.