So many good responses here. I think you could write the story both realistically and plausibly. In your description, the "jump drive" is just fast sub-light travel- no bending or bridging of space-time, no teleportation mechanics. They're just flying fast, like, real fast. So slow them down without destroying then in the process.
Interdiction rockets that chase down the target, attach, then counter-thrust to stop them? Deploy an advanced substance to snare them (e.g. a liquid or polymer web to brake their kinetic energy mid-flight)? Disable their thrust (e.g. with an EMP or weapon) then brake them (or match speed and mate with their craft).
I think since it's traditional sub-light travel, it's more akin to "how do I stop the train" rather than the usual sci-fi "how do I drop them out of warp" or "how do I intercept this wormhole".