If the crates are conductive, and you put magnets in your cargo scoop, they generate eddy currents and a braking force proportional to the relative speed of the crate.
Once the crates are down to a reasonable relative speed, a net can finish the job.
Well, that's an idea! Hook up a complex magnet array to a swivel, and you could easily make the break and net from the same component. I suppose you could redline it to perform in maneuver conditions. Now I have the missing component!