Frabby
I don't know if the following has been considered by Mica/David yet as part of the infrastructure upgrade.
The thought occurred to me that while agents are members of the starbase personnell, operatives are not. The differences between them should be greater. In fact, operatives are intruders into the starbase compound and have to remain hidden.
Agents should therefore be premium at espionage and hacking stuff.
Operatives would rather be useful for assassination and sabotage, perhaps some espionage, but have a hard time hacking or contacting starbase personnell (such as for recruiting agents).

My main point, however, is this: An operative's job of remaining hidden will be much easier in a garden world trade center starbase (where he can easily mingle with the locals) than in an enclosed science station on an airless moon.
There should be a background mission risk modifier for operatives based on population density of the world and "openness" of the starbase, i.e. level of interaction with a local population. A starbase with dozens or even hundreds of shuttle ports and merchandising complexes can hardly claim to be a restricted area even with a high security crackdown.
The race of the operative compared to the race of the resident population and starbase personnell would also play a role in this.

This will obviously only apply to operatives. It could be a modifier to the success/caught chances or the costs of undertaking a mission.