Maybe agents could come in neutral/light/dark varieties. Each "Agent" type representing an archetype like nyotas described. (merchant/barabarian/dark cultist/light worker, etc.) And of course you as the player can use Power to corrupt or otherwise manipulate them...and perhaps take direct control if you corrupt them far enough into your evil clutches. (presumably easier to gain control over dark cultist types)
I'd definitely like some agents (maybe 1 to 3) to be under the player's direct control. Give the player something to click and move each turn, to reduce the number of "just hit end turn" turns.
I agree it would be very reasonable to have all agents already exist on the map, and the player to corrupt/take-control-of the agents they want, like they do with enthralling nobles. It may allow agents to have some pre-existing histories (connection to societies, likings and disliking with established nobles).
As I mentioned to nyotas, things will take a bit, and I'll need to see what works for a first version. Hopefully many versions can expand on this, and allow the noble-enthralled and the agent-enthralled to work together to make both as exciting to play with as possible.
Thanks to both of you for your suggestions though, and feedback on what the playerbase would like to see. Good to have a direction to follow.