1. If your configuration allows, you could put a spring on the end of the lead nut's guide rod. You would just have to make sure that the spring isn't strong enough to push the nut backward (99.99% sure that this won't ever happen).
2. You could set up the switch that stops the motor to trigger a bit before the wheels stop rotating. You can set the switch however far you want, but generally, 2-3 rotations worth of distance on the screw should work.
3. You could rewire the switch that stops the motor to make an eddy current brake. This will make the motor resist rotation after the switch is triggered. There is an illustration of how to wire an eddy brake in the SciOly Wiki, on the Battery Buggy page, under Braking Systems.
4. This doesn't make the buggy slow down on its own, but making your buggy lighter can help considerably in stopping quicker. The lighter the buggy, the more effective any braking system becomes for a vehicle moving the same speed.
You can also combine the ideas on this list to make your braking system work as best as it can. For example, my buggy uses both 2 and 3.