I like the idea of the Agents knowing to some degree when and where the Heroes are going to arrive. Played right it could add a lot of tension. If jump-drive has a predetermined destination I imagine that once it kicks in your ship is locked into its path--only being able to be knocked from it or, as you suggest , something is done to slow the Heroe's ship.

How it could work dramatically: the Heroes slip away from the Agents using the jump-drive. The Agents quickly activate some device (a pulsing buoy, technobabble) in the last place the ship was seen. It lets off three thumps in every direction. The Agent's ships rock back with each pulse after which they retrieve the buoy. A little dialogue about waiting for the pulses to dissipate before engaging their own jump-drive ("we don't want to get caught in the pulse's wake") and they're off.

Cut to the Heroes ship in the jump-space: They think they've made a quick escape but the ship stumbles and an alarm goes off. A quick look at their instruments tells them the ship is dropping speed. This happens twice more-the three pulses catching up to them-each time slowing them not quite out of jump-space but enough to know they're heading into the trouble they thought they's just outrun.

This could be used in universe as a something that is rarely deployed because it does affect every ship that engaged jump-drive in that area within a certain timeframe (pick your area of effect and time factors for best storytelling) so it's quite a statement as to how badly the Agents want to thwart the heroes. When the 'pulse buoy' is used, yes, you may slow them down but you may have also affected local commerce, local military and even other Agents in the area by using it. It's effective but costly. You've just broadcast your location and the desperation of your goals to everyone in that area.